title: 32_rep4_AzuNIL_Al

city: Ithaca

first: Susan

middle: R.

last: McCouch

address: 162 Emerson Hall

department: Plant Breeding & Genetics

institute: Cornell University

data_processing:
Raw RNA-Seq reads were processed to remove adaptor and low quality sequences using Trimmomatic
RNA-Seq reads longer than 40 bp were kept
Reads that aligned to the ribosomal RNA database (Quast et al. 2013) using Bowtie were discarded.
The resulting, high-quality reads were aligned to the MSUv7.0 rice genome annotation using HISAT (Kim et al. 2015).
Following alignments, raw counts for each rice gene were derived and normalized to reads per Kilobase of exon model per million mapped reads (RPKM).
Genome_build: Nipponbare (Oryza sativa) MSU version 7
Supplementary_files_format_and_content: RNAseq raw counts

source_name: rice roots

growth_protocol: 40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 μM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.

extract_protocol:
Total RNA was isolated using the QIAGEN RNeasy Mini Kit according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols and multiplexed 16x

value: AZU[IR64121] (near-isogenic line)

value: Al

tag: biological rep


title: 28_rep4_AzuNIL_control

status: Public on Sep 01 2017

type: SRA

state: NY

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Oryza sativa

tag: genotype

tag: treatment

value: control


title: 30_rep4_IR64NIL_Al

value: IR64[AZU12.1] (near-isogenic line)


title: 29_rep4_IR64_Al

value: IR64 (indica)


title: 27_rep4_Azucena_control

value: Azucena (tropical japonica)


title: 26_rep4_ IR64NIL_control


title: ARC-Fast-3

city: Box 289, Addenbrooke’s Hospital

first: Joseph

last: Polex-Wolf

state: Cambridgeshire

address: Wellcome Trust-MRC Institute of Metabolic Science

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

data_processing:
Basecalls performed using CASAVA 1.7
Reads were aligned to the mouse genome (GRCm38) using Tophat v2.0.11
Counts were determined using Cufflinks v2.2.1
Count normalisation was performed using the edgeR and limma packages in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: Reads Per Kilobase of transcript per Million mapped reads (RPKM)

organism: Mus musculus

source_name: laser-captured hypothalamic nucleus (region)

extract_protocol:
Hypothalamic nuclei were laser-capture microdissection from cryosections using a P.A.L.M Microlaser system, and RNA extracting using the miRNeasy micro RNA extraction kit (Qiagen).
Total RNA was amplified using an Ovation RNA-Seq System V2 (NuGEN), after which cDNA libraries were prepared using the Encore Rapid DR Multiplex System (NuGEN).

treatment_protocol: Wild-type male C57/BL6 mice were either ad-libitum fed or fasted for 24-hours prior to brain dissection.

tag: strain

tag: nutritional state

value: 24 hour fasted

tag: tissue

value: arcuate nucleus

tag: gender

value: male


title: 25_rep4_IR64_control


title: 24_rep3_AzuNIL_Al


title: 23_rep3_Azucena_Al


title: 22_rep3_IR64NIL_Al


title: 18_rep3_ IR64NIL_control


title: 19_rep3_Azucena_control


title: 16_rep2_AzuNIL_Al


title: 14_rep2_IR64NIL_Al


title: 21_rep3_IR64_Al


title: 13_rep2_IR64_Al


title: 8_rep1_AzuNIL_Al


title: 31_rep4_Azucena_Al


title: 11_rep2_Azucena_control


title: 12_rep2_AzuNIL_control


title: 10_rep2_ IR64NIL_control


title: 9_rep2_IR64_control


title: 15_rep2_Azucena_Al


title: 6_rep1_IR64NIL_Al


title: 5_rep1_IR64_Al


title: 3_rep1_Azucena_control


title: 7_rep1_Azucena_Al


title: 2_rep1_ IR64NIL_control


title: 1_rep1_IR64_control


title: 20_rep3_AzuNIL_control


title: Lean ATM Exo5

city: La Jolla

first: Wei

last: Ying

state: CA

address: 9500 Gilman Dr, Stein Clinical Research Building, Room 225

institute: UC San Deigo

data_processing:
miRNA-seq reads were quality-assessed with FastQC and MultiQC, then trimmed with Trimmomatic 0.30 and subsequently aligned with NovoAlign to all mouse miRNA hairpin sequences in release 21 of miRBase.
The resulting alignments were tabulated with a python script to generate per-miRNA counts.
Using a custom analysis pipeline developed in an R-kernel Jupyter Notebook, very lowly expressed miRNAs and those not represented in at least ~1/3 of samples were filtered, and the remaining data were subjected to TMM (trimmed mean of M values) normalization using the EdgeR package in Bioconductor.
Principal component analysis demonstrated that negligible library-size or batch effects remained.
The voom method was used in conjunction with the limma package to estimate precision weights for all observations and then identify differentially expressed miRNAs.
Genome_build: release 21 of miRBase
Supplementary_files_format_and_content: tab-delimited text files including identified miRNAs, fold change, p-value, AverExpr…

source_name: adipose tissue macrophages

growth_protocol: Adipose tissue macrophages were cultured in IMDM/10% exosome-free FBS for 72 hours, and then the exosomes were purified from medium by ultracentrifugation.

extract_protocol:
Total RNAs were extracted by using miRCURY RNA isolation kit-Biofluids.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose

tag: cell type

value: macrophage

tag: obesity status

value: lean

tag: age


title: Lean ATM Exo7


title: 17_rep3_IR64_control


title: Lean ATM Exo4


title: Lean ATM Exo2


title: Lean ATM Exo3


title: RI-2 miRNA

city: Hangzhou

first: Heng-Mu

last: Zhang

address: 198 Shiqiao Road

department: Institute of Virology and Biotechnology

country: China

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
The 3‘adaptors were trimmed by FASTX Toolkit (fastx_clipper 0.0.14) with parameters -l 18. Perl script developed by ourselves was used to filter the low quality reads.
All clean reads were aligned to miRBase (version 21) by miRDeep2 with default parameters
Genome_build: miRBase V20(http://www.mirbase.org/index.shtml)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: leaf cells

growth_protocol: Small brown planthoppers (Laodelphax striatellus) were raised on rice plants (cv. Wuyujing 3) in a growth room

extract_protocol:
Tissue samples were stored at -80°C prior to use, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries according to Illumina Truseq miRNA libraries construction protocol.
RNA libraries were prepared for sequencing according toIllumina Truseq miRNA libraries construction protocol

treatment_protocol: Rice seedlings at the three-leaf stage were inoculated by viruliferous small brown planthoppers

value: Infected leaf cells


title: CK-3 miRNA

value: mock leaf cells


title: RI-1 miRNA


title: RI-3 miRNA


title: CK-1 miRNA


title: CK-2 miRNA


title: CK-3 mRNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by fastx_toolkit-0.0.13.2, then mapped to whole genome using SOAP with parameters: maximum number of mismatches allowed = 2bp， number of valid alignments per read pair (-k) = 40
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated.
Genome_build: http://rice.plantbiology.msu.edu/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Tissue samples were stored at -80°C prior to use, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Lean ATM Exo1


title: 4_rep1_AzuNIL_control


title: Obese ATM Exo6

value: obese


title: CK-2 mRNA


title: Obese ATM Exo5


title: AGS_ChIPseq_H3K4me3 (DN1705230053LD1)

city: Shanghai

first: Bin

last: Xiang

address: Building 3, 4218 Jinke Road, Pudong

institute: novartis institutes for biomedical research

library_source: genomic

data_processing:
The ChIP-seq was conducted in the human cancer cell line H358 and AGS cells using FXR1, FXR2, STAT1/3 and H3K4me3 specific antibodies on the platform Illumina HiSeq 2000.
ChIP-seq data quality was analyzed using FastQC. FXR1 or histone mark binding genomic regions (called ChIP-seq peaks) were identified by Model-based Analysis of ChIP-Seq (MACS) algorithm using the default p-value cutoff of 1e-5.
Read length: 50bp (adaptor occupies 6~8 bp in each SE read)
Reads in the fastq file were trimmed by 5 base pairs in the 5´-end, and then mapped to the reference human genome (HG19) with the algorithm Burrows-Wheeler Aligner (BWA). The mapped reads were filtered with BamTools using criteria that the mapping quality should be >= 30.
The distribution of FXR1 ChIP-seq peaks were investigated by the annotations on the human genome. The peaks were binned into three groups according to the positions relative to annotated genes: promoter, gene body, and intergenic region. The aggregation signals of FXR1,FXR2, STAT1/3 and H3K4me3 across the whole genome were plotted using the ceasBW tool.
A hub for UCSC genome browser was constructed in order to investigate the detailed information of the peaks. The summit positions of the FXR1 ChIP-seq peaks were extended to 50 bp both up- and down-stream by MACS to construct the BED files. After converting the BED files into FASTA files using the reference genome sequence, the BED files were provided to MEME.
Genome_build: HG19
Supplementary_files_format_and_content: MACS peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: Human  cancer cell line

growth_protocol: Human cancer cell line H358 and AGS were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS, GIBCO) and 100 U/mL penicillin-streptomycin (GIBCO) in humidified incubator set at 37°C with 5% CO2 using the standard techniques

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: AGS

value: gastric cancer cell line

tag: chip antibody

value: anti-H3K4me3 (CST, 9727)


title: Obese ATM Exo7


title: Obese ATM Exo4


title: AGS_ChIPseq_STAT3 (DN1705230051LD1)

value: anti-STAT3 (Santa Cruz, sc-482; CST, 12640S)


title: Lean ATM Exo6


title: Obese ATM Exo2


title: AGS_ChIPseq_STAT1 (DN1705230049LD1)

value: anti-STAT1 (Santa Cruz, sc-345; CST, 14994S)


title: Obese ATM Exo3


title: AGS_ChIPseq_FXR2 (DN1706260060LD01)

value: anti-FXR2 (Invitrogen, PA5-28979)


title: Setd2 KO_deep_sequencing

first: Ni

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

description: Setd2 KO

data_processing:
Raw reads were subjected to quality control (QC) to determine if a resequencing step is needed.
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5).
RNA-seq reads were mapped to mouse transcripts (Ensembl, release 65) and genome(mm9) using the TopHat2(Trapnell et al., 2009) allowing 2bp mismatches per 25bp seed.
rMATS.3.0.9 (Shen et al., 2012) (http://rnaseq-mats.sourceforge.net/;version 3.0.9) was use to identify SETD2-regulated differential alternative splicing events corresponding to all five types of alternative splicing patterns. Putative SETD2-regulated alternative splicing events were identified as those with significant difference in inclusion levels between knock and control, at P valu<0.05, FDR<20%.
Genome_build: mm9

source_name: Intestine

growth_protocol: All mice were maintained in specific-pathogen-free (SPF) facility.

extract_protocol:
Intestines were removed, flash frozen on dry ice and RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd. We mapped RNA-seq reads to mouse transcripts (Ensembl, release 65) and genome(mm9) using the TopHat2(Trapnell et al., 2009) allowing 2bp mismatches per 25bp seed.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment

value: APCmin; Setd2IEC-/-

value: post natal 2 months

value: intestine


title: Obese ATM Exo1


title: AGS_ChIPseq_Input (DN1705230044LD1)

value: none (input)


title: AGS_ChIPseq_FXR1 (DN1706260059LD01)

value: anti-FXR1 (Sigma, HPA018246)


title: control_deep_sequencing

description: control

value: APCmin


title: H358_ChIPseq_H3K4me3 (DN1705230043LD1)

value: non small cell lung cancer cell line


title: CK-1 mRNA


title: Setd2 KO_RNA-seq

description: Setd2 KO

data_processing:
Raw reads were subjected to quality control (QC) to determine if a resequencing step is needed.
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5).
Use  Bowtie2  to map clean reads to reference gene and use  BWA to reference genome.
RSEM  was used to computed maximum likelihood abundance estimates. FPKM  method is used in calculated expression level.
Use NOISeq to screen differentially expressed genes between two groups.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.

extract_protocol:
Intestines were removed, flash frozen on dry ice and RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd. Transcriptome reads from RNA-Seq experiments were mapped to the reference genome (mm10) by using BWA/Bowtie tool. Genes expression level is quantified by a software package called RSEM.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background


title: H358_ChIPseq_STAT3 (DN1705230041LD1)


title: control_RNA-seq

description: control


title: bel mutant, rep2

city: Tallahassee

first: Wu-Min

last: Deng

state: Florida

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

description:
bel trans-heterozygous mutant
small non-coding RNAs

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt and low-complexity or low-quality sequenced reads were removed by sickle.
Ribosomal, small nucleolar, tRAN and miRNA sequenced reads (their reference sequences were downloaded from Flybase) were removed from total sequenced reads using bowtie (bowtie -a --best --strata -v 1 --un).
The processed sequencing reads were aligned to Drosophila genomic reference sequences (dm3) and BDGP Drosophila transposable element (TE) reference sequences using bowtie (-a -v 0 -m 7 for dm3; -a -v 0 -m 1 for TEs).
Reads Per Kilobase of TE per Megabase of library size (RPKM) were calculated for TE expression analysis.
Genome_build: BDGP assembly R5/dm3
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

organism: Drosophila melanogaster

source_name: Ovary

extract_protocol:
Total RNA from 2-day-old Drosophila ovaries was isolated using Trizol Reagent (Invitrogen).
Small RNAs libraries were prepared according to instructions for Illumina TrueSeq Small RNA sample prep kit with some modifications that pre-annealing of terminator oligonucleotides to Drosophila 2S rRNA was performed prior to 5´ adapter ligation and reverse transcription for efficiently depleting 2S rRNA sequences.

value: female

value: Ovary

value: two-day old adults


title: bel mutant, rep1


title: bel mutant, rep3


title: tc_psh1_cac2_1_m

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description:
cse4_psh1_cac2_1_m_ip_tc.bw
cse4_psh1_cac2_2_m_ip_tc.bw

data_processing:
Base calls were performed using bcl2fastq.
Paired-end reads from an Illumina NextSeq were aligned to version sacCer3 of the yeast genome from UC Santa Cruz using bowtie2 with -k 2. Concordant alignments were analyzed in R using Bioconductor to generate coverage and normalize the data in Reads Per Million.
Ratio tracks of IP/Total Chromatin in bigwig format were create by adding a value of 1 to the RPM coverage of the individual tracks and then taking the quotient for display in log2 format.
Two different experiments were performed, with replicates, giving rise to two replicate groups as noted. For replicate group m, the are two IP replicates but only one of the matching total chromatin replicates was sequenced, thus the IPs for that group share a background as indicated.
Genome_build: sacCer3

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Overnight cultures of WT and mutant strains grown in duplicate in appropriate raffinose media. Overnight cultures were diluted to OD600 of 0.1.

extract_protocol:
Cells were lysed by bead beating for 1 hour at 4°C in FA-Lysis SDS buffer (50mM Hepes (pH7.5), 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.2% SDS, protease inhibitors) and centrifuged to remove cell debris. The lysate was sonicated using a Biorupter for 30 minutes, 30 seconds on/off, medium intensity. Protein concentration was determined and samples were normalized before proceeding with the ChIP. 30% and 3.5% of total chromatin extract were used for the IP and the input samples respectively.
Libraries were prepared using the KAPA HTP Library Prep Kit for Illumina and Bioo Scientific NEXTflex DNA barcodes. The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies). Post amplification size selection was performed on libraries where there was enough available material to do so using a Pippin Prep (Sage Science). Libraries were re-quantified, normalized, pooled and sequenced on an Illumina NextSeq 500 instrument as Mid Output 75bp paired read run.

treatment_protocol: After 2h at 30°C, Cse4 overexpression was induced by adding galactose to a final concentration of 4% and cultures were grown at 30°C for 6h. Cells were fixed in 1% formaldehyde for 15 minutes at room temperature, then quenched with glycine (final concentration 0.125M) for 5 minutes. Cells were washed twice with cold TBS, frozen in liq. N2, and stored in -80°C until used.

tag: type

value: total chromatin

tag: epitope

tag: replicate group


title: H358_ChIPseq_Input-2 (DN1705230036LD1)


title: HCT116_ML00754792_No heatshock (SAE034019)

city: Cambridge

first: Pooja

last: Shah

state: MA

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio (OSA v4 _ http://omicsoft.com)
Based on the negative binomial distributions of sequencing read counts Omicsoft’s incorporated DESeq2 v1.10.1 was used for differential gene expression. Differential gene expression and false discovery rate corrected p-values of <0.05 and fold-change values greater than 2 were considered significant
Genome_build: Human Genome (Human.B37.3)
Supplementary_files_format_and_content: mRNA FPKM count data for each sample

source_name: HCT116_ML00754792_No heatshock

extract_protocol:
RNA was isolated from biological triplicates with RNAeasy protocols (Qiagen RNeasy_96). The purity and quantity of total RNA samples were determined by absorbance readings at 260 and 280 nm using a NanoDrop ND-1000 UV-Vis spectrophotometer (ThermoFisher Scientific). The integrity of total RNA was assessed by capillary electrophoresis using an Agilent Bioanalyzer 2100 (Agilent)
TruSeq Stranded mRNA Library Kit (Illumina) was used for library construction
RNA Sequencing was performed on the HiSeq (Illumina) with 30 million, 50-base pair-end reads per sample

treatment_protocol: Cells were treated by 0.01% DMSO or 0.5 μM ML-792 at 8 h, 16 h, 48 h, or HCT116 cells harboring tet-inducible shRNAs were treated with Doxycycline for 96 h. For heat shock study, HCT116 cells were treated with 0.01% DMSO or 0.5 μM ML-792 for 2 h followed by treatment for 0.5 h at 43 ⁰C (heat shock)  and recovery at 37 ⁰C for 1 h

value: colorectal cancer cell line HCT116

tag: dosage

tag: time


title: HCT116_ML00754792_No heatshock (SAE034025)


title: HCT116_DMSO_No heatshock (SAE034016)

source_name: HCT116_DMSO_No heatshock

value: DMSO


title: HCT116_DMSO_No heatshock (SAE034010)


title: Wild type, rep2

description:
control sample
small non-coding RNAs

tag: genotype

value: wild type (W1118)


title: HCT116_ML00754792_With Heatshock (SAE032542)

source_name: HCT116_ML00754792_With Heatshock

tag: treatment

tag: regimen

value: 2hr then heatshock for 0.5hr, the recover 1hr, all under drug treatment


title: cse4_ip_psh1_cac2_2_m

tag: strain

value: ip


title: Wild type, rep3

description:
control sample
small non-coding RNAs

tag: tissue


title: Wild type, rep1

description:
control sample
small non-coding RNAs

tag: gender


title: cse4_ip_psh1_cac2_1_m


title: HCT116_DMSO_No heatshock (SAE034013)


title: HCT116_ML00754792_With Heatshock (SAE032540)


title: tc_psh1_1_a


title: tc_psh1_2_m

description:
cse4_psh1_1_m_ip_tc.bw
cse4_psh1_2_m_ip_tc.bw


title: HCT116_DMSO_With Heatshock (SAE032533)

source_name: HCT116_DMSO_With Heatshock


title: HCT116_ML00754792_With Heatshock (SAE032537)


title: HCT116_DMSO_With Heatshock (SAE032530)


title: cse4_ip_psh1_2_m


title: cse4_ip_psh1_1_a


title: H358_ChIPseq_STAT1 (DN1705230039LD1)

tag: cell type

value: anti-STAT1 (Santa Cruz, sc-345; CST, 14994S)


title: HCT116_ML00754792_No heatshock (SAE034022)


title: HCT116_DMSO_With Heatshock (SAE032527)


title: MDAMB231_DMSO_16hr (SAE008047)

value: Breast cancer cell line MDAMB231


title: tc_cac2_1_a


title: cse4_ip_psh1_1_m


title: cse4_ip_cac2_1_a


title: MDAMB231_DMSO_16hr (SAE008045)


title: MDAMB231_DMSO_16hr (SAE008046)


title: cse4_ip_cac2_1_m


title: MDAMB231_ML00754792_16hr (SAE008040)


title: COLO205_DMSO_16hr (SAE008034)

value: colorectal cancer cell line COLO205


title: tc_cac2_1_m

description:
cse4_cac2_1_m_ip_tc.bw
cse4_cac2_2_m_ip_tc.bw


title: MDAMB231_ML00754792_16hr (SAE008041)


title: cse4_ip_wt_2_a

value: wt


title: cse4_ip_cac2_2_m


title: COLO205_DMSO_16hr (SAE008033)


title: MDAMB231_ML00754792_16hr (SAE008039)


title: COLO205_DMSO_16hr (SAE008035)


title: tc_wt_2_a


title: COLO205_ML00754792_16hr (SAE008029)


title: cse4_ip_wt_1_a


title: tc_wt_1_m


title: tc_wt_1_a


title: COLO205_ML00754792_16hr (SAE008028)


title: COLO205_ML00754792_16hr (SAE008027)


title: vir bulk

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
Sample 9
bulk transcriptomics

data_processing:
Sequenced reads were converted to SAM files to couple them with the cell and molecular barcodes using Drop-seq_tools v1.12. They were further trimmed for SMART adapter and poly(A) remnants.
The filtered reads were mapped with STAR. The Drop-seq_tools v.1.12 were used to add gene annotations, detect bead synthesis errors and calculate the Digital Gene Expression matrices.
Bulk mRNA reads were mapped with STAR. Gene counts were computed with htseq-count.
Genome_build: Drosophila_melanogaster.BDGP6 & Drosophila_virilis.GCA_000005245.1
Supplementary_files_format_and_content: Digital Gene Expression matrices contain UMI counts per cell and per gene. Htseq-counts measure gene abundances in mRNA samples (read counts)

molecule: polyA RNA

organism: Drosophila virilis

source_name: mRNAseq whole embryo

growth_protocol: Egg lays occurred in 1 hour intervals; embryos were aged for 2:30 hours (D. melanogaster) or 3:30 hours (D. virilis) at room temperature.

extract_protocol:
Whole, live embryos were dissolved in TRIZOL, shock-frozen in liquid nitrogen, then total RNA was extracted
Libraries were generated from 200 ng RNA with NEBNext Ultra RNA Library Prep Kit for Illumina using poly(A) mRNA magnetic isolation.
mRNAseq, unstranded

treatment_protocol: Dechorionated embryos were staged and stage 6 embryos hand-picked into ice-cold PBS-Triton 0.1%.

tag: developmental stage

value: stage 6

value: intact embryo

value: D.vir. we

tag: fixation

value: live, not fixed


title: HCT116_DMSO_16hr (SAE008022)

tag: cell line


title: HCT116_DMSO_16hr (SAE008021)


title: HCT116_ML00754792_16hr (SAE008017)


title: SKOV_FAV_pcDNA3

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

description: poly-A RNA, fragmented (200nt)

data_processing:
Reads were treated with Cutadapt (using parameters -g GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG --minimum-length 2) and Trimmomatic (with TRAILING:30)
The resulting reads were aligned to the build hg38 using STAR (--outSAMprimaryFlag AllBestScore, --alignIntronMax 1250000), unmapped reads being re-aligned with Bowtie2 (-q -I 13).
CoCo (http://gitlabscottgroup.med.usherbrooke.ca/scott-group/coco) was used to produce read counts per genes and associated CPM and TPM values from the Ensembl (v87) annotation modified with CoCo.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated-value (csv) files holding the name of every gene and their abundance value (raw counts, CPM or TPM) for each dataset

source_name: SKOV3ip1 cell line

growth_protocol: grown in DMEM/F12 (50/50) medium (Wisent), supplemented with 10 % fetal bovine serum and 2 mM L-glutamine. Cell propagation and passaging were as recommended by ATCC (American Type Culture Collection). Cells were trypsinized and collected in 5X106 pellets resuspended in 700ul TRIzol (Ambion) and kept at -80°C until RNA extraction

extract_protocol:
cDNA library produced with retroviral RT
The poly(A) RNA was isolated and purified from 5ug DNA-free total RNA using NEBNext Poly (A) mRNA Isolation Module (New England Biolabs) according to the manufacturer protocol.
Library preparations were performed using the NEBNext Ultra directional RNA library Prep Kit for Illumina (New England Biolabs) in order to generate RNA-seq library from 100 ng of purified RNA. The RNA and library quality were verified using Agilent Bioanalyzer (Agilent Technologies).

value: Ovarian serous cystadenocarcinoma

value: Lipofectamine 2000 treated, empty pcDNA3 vector transfected


title: SKOV_FAV_LF

description: poly-A RNA, fragmented (200nt)

value: Lipofectamine 2000 treated


title: HCT116_ML00754792_16hr (SAE008016)


title: SKOV_FRV_2

description: Total RNA ribodepleted, fragmented (200nt)

extract_protocol:
cDNA library produced with retroviral RT
RNA was ribodepleted from 5ug DNA-free total RNA using Ribo-zero Gold (Illumina) according to the manufacturer protocol.
Library preparations were performed using the NEBNext Ultra directional RNA library Prep Kit for Illumina (New England Biolabs) in order to generate RNA-seq library from 100 ng of purified RNA. The RNA and library quality were verified using Agilent Bioanalyzer (Agilent Technologies).


title: SKOV_FRV_1


title: SKOV_FRT_2

extract_protocol:
cDNA library produced with TGIRT (thermostable group II reverse transcriptase)
Purified total RNA was ribodepleted by using a RiboZero Gold (Human/Mouse/Rat) kit (Illumina). The resulting ribodepleted RNAs were fragmented with an NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) by incubation at 94°C for 7 minutes and were then treated with T4 polynucleotide kinase (T4PNK; Epicentre) to remove 3’ phosphates or 2’, 3’ cyclic monophosphates.
cDNAs were synthesized via TGIRT template-switching with either 0.5 or 1µM TGIRT-III reverse transcriptase (Ingex, LLC) for 15 min at 60o C, during which a DNA oligonucleotide containing the complement of an Illumina Read 2 sequencing primer-binding site becomes seamlessly linked to the 5’ cDNA end. After reaction cleanup, a 5’ adenylated DNA oligonucleotide containing the complement of an Illumina Read 1 sequencing primer-binding site is then ligated to the 3’ cDNA end with Thermostable 5’ AppDNA / RNA Ligase (New England Biolabs). Properly ligated cDNAs were amplified by PCR (12 cycles) to synthesize the second strand and add Illumina flowcell capture and index sequences. Libraries were size-selected with Ampure XP beads (Beckman-Coulter) and evaluated on an Agilent 2100 Bioanalyzer


title: umbilical cord

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

data_processing:
Illumina base calling, demultiplexing, and FASTQ conversion with CASAVA-1.8.2
alignment to the genome reference using STAR
reads counted on the Ensembl release 75 gene models with htseq-count 0.6.1p1
Genome_build: hg19
Supplementary_files_format_and_content: htseq-count output, two-column text file with Ensembl gene identifier and read count columns

source_name: umbilical cord

extract_protocol:
TRIZOL
Ribodepletion followed by default Illumina RNA-Seq for HiSeq2000 (TruSeq)

value: umbilical cord


title: vascular smooth muscle cells

source_name: derived from mesenchymal stem cells, female, 23 years

value: vascular smooth muscle cells


title: SKOV_FRT_1


title: HCT116_ML00754792_16hr (SAE008015)

value: colorectal cancer cell line HCT116


title: SKOV_URT_1

description: Total RNA ribodepleted, non-fragmented

extract_protocol:
cDNA library produced with TGIRT (thermostable group II reverse transcriptase)
Purified total RNA was ribodepleted by using a RiboZero Gold (Human/Mouse/Rat) kit (Illumina) and the resulting RNA were then used directly for library construction.
cDNAs were synthesized via TGIRT template-switching with either 0.5 or 1µM TGIRT-III reverse transcriptase (Ingex, LLC) for 15 min at 60o C, during which a DNA oligonucleotide containing the complement of an Illumina Read 2 sequencing primer-binding site becomes seamlessly linked to the 5’ cDNA end. After reaction cleanup, a 5’ adenylated DNA oligonucleotide containing the complement of an Illumina Read 1 sequencing primer-binding site is then ligated to the 3’ cDNA end with Thermostable 5’ AppDNA / RNA Ligase (New England Biolabs). Properly ligated cDNAs were amplified by PCR (12 cycles) to synthesize the second strand and add Illumina flowcell capture and index sequences. Libraries were size-selected with Ampure XP beads (Beckman-Coulter) and evaluated on an Agilent 2100 Bioanalyzer


title: serum

source_name: female, 23 years

tag: sample type

value: serum


title: cse4_ip_wt_1_m


title: vena cava

source_name: DILV (double inlet left ventricle), male born 2006

value: vena cava


title: plasma

value: plasma


title: right atrium

source_name: cAVSD, AV-channel, Trisomy 21, female born 2008

value: right atrium


title: HCT116_DMSO_16hr (SAE008023)

value: DMSO


title: osteocytes

value: osteocytes


title: placenta

source_name: placenta

value: placenta


title: platelets

value: platelets


title: neutrophils

source_name: male, 30 years

value: neutrophils


title: muscle

source_name: ear, male, 21 years

value: muscle


title: mesenchymal stromal cells

source_name: extracted by abdominal lipo-aspiration, female, 23 years

value: mesenchymal stromal cells


title: WAS lymphoblastoid cells

source_name: EBV-immortalized from whole blood, male, 2 years

value: WAS lymphoblastoid cells


title: lymphoblastoid cells

source_name: EBV immortalized from whole blood, male, 21 years

value: lymphoblastoid cells


title: non-sibling (19)

first: Giordano

last: Lippi

address: 9500 Gilman Drive

department: Neurobiology

institute: University of California, San Diego

description: miRNA

data_processing:
Reads mapped using mirDeep2 to miRBase release 19 mature miRNA dataset
Read counts quantile normalized using preprocesscore from the Bioconductor 3.1 library in R 3.2
Genome_build: miRBase r19
Supplementary_files_format_and_content: Excel file; qNorm read counts and log2 fold change

organism: Xenopus laevis

source_name: Neuronal AOB tissue

extract_protocol:
Total RNA was extracted from frozen cryosectioned (50 μm) tissue with the “Recover All Total Nucleic Acid” isolation kit.
mRNA-seq libraries were prepared using the Illumina mRNA-seq Sample Preparation kit following the manufacturer’s instructions.

treatment_protocol: The AOBs of 15 larvae (stage 45) raised in sibling, orphan, or non-sibling conditions

value: 15-day-old larvae

value: accessory olfactory bulb


title: HUVEC

source_name: human umbilical vein endothelial cells

value: HUVEC


title: sibling (18)

description: miRNA


title: fibroblasts

source_name: buttock biopsy, primary cells, male, 21 years

value: fibroblasts


title: orphan (17)

description: miRNA


title: SKOV_URT_2

description: Total RNA ribodepleted, non-fragmented

value: Ovarian serous cystadenocarcinoma


title: adipose tissue

source_name: abdominal lipo-aspiration for mesenchymal stem cell extraction, female, 23 years

value: adipose tissue


title: endothelial progenitor cells

source_name: umbilical cord blood

value: endothelial progenitor cells


title: cortex

source_name: epilepsy patient, female, 38 years

value: cortex


title: chondrocytes

value: chondrocytes


title: ES-E14-Suz12

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

institute: NIH

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were mapped to the mm9 genome assembly using Bowtie2 version 2.2.4 with the default configurations.
RNA-seq reads were mapped to the mm9 genome assembly using TopHat version 2.0.13 (Trapnell C, et.al 2009) with the default configurations.
peaks were called using SICER version 1.1 ( Zang et al, 2009) with the following setting: redundancy threshold (1), window size (200), fragment size (150), effective genome fraction (0.74), gap size (600),FDR (0.05) .
FPKM(RPKM) and differential expression analysis was done using Cufflink/Cuffdiff (Trapnell C, et.al 2009) with multi-reads correction and geometric normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include peak values for each Sample;tab-delimited text files includes FPKM values for each Sample.

growth_protocol: ESCs grow on gelatin-coated dishes in ES medium (DMEM, 15% HyClone FBS, GlutaMAX, MEM nonessential amino acids, sodium pyruvate, leukaemia inhibitory[LIF], β-mercaptoethanol)

extract_protocol:
For ChIPSeq,cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments.  Lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen).
For ChIPSeq,  10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with  Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol. the NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) were used to process RNA-Seq samples following the manufacturer’s protocol.

treatment_protocol: Cells were transfected with control and Spt6 siRNA with RNAiMAX according to manufacturer's protocol.

value: embryonic stem cell, blastocyst derived

tag: chip antibody


title: PC_2

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

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 mm10 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: C2C12 was cultured in growth medium, DMEM (Hyclone) supplemented with 10% fetal bovine serum (Hyclone) and 1% pencillin/streptomycin (Hyclone). To arrest cell cycle of C2C12 and model the quiescent state, C2C12 were trypsinized and suspended in semi-solid medium . A final concentration of 3×105 per ml were cultured in DMEM containing 1.5% methylcellulose (4000 centipoise, Sigma), supplemented with 20% FBS.

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

treatment_protocol: FoxM1was knockdowned in C2C12 through short hairpin RNA (shRNA).

value: mouse myoblast cell line

tag: cell status

value: Activated

tag: intervention

value: shControl


title: PFM_1


title: Panc_MLN_r3

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: pancreatic cancer cells PANC-1 (ATCC® CRL-1469™)

growth_protocol: Human PANC-1 cells (ATCC® CRL-1469™) were obtained from the American Type Culture Collection (ATCC, Rockville, MD) and maintained according to their recommendations.

extract_protocol:
RNA was isolated using RNeasy mini kit with optional on column DNA digestion (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PANC-1 cells that were treated for 24hrs with vehicle, chaetocin (30nM), MLN8237 (90nM) or combination (30 + 90nM, CH + MLN8237 respectively).

tag: passage


title: PFM_3


title: ADA-SCID lymphoblastoid cells

source_name: lymphoblastoid cells, EBV-immortalized from whole blood, male, 25 years

value: ADA-SCID lymphoblastoid cells


title: PFM_2


title: Panc_MLN_r1


title: cartilage

source_name: male, 21 years

value: cartilage


title: PC_3


title: QFM_2

value: Quiescent


title: Panc_MLN_r2


title: QFM_1


title: PFM_4


title: ES-E14-UTX


title: PC_1


title: QC_2


title: QFM_3


title: QFM_4


title: HUAEC

source_name: human umbilical arterial endothelial cells

value: HUAEC


title: QC_1


title: Panc_DMSO_r2

value: vehicle (DMSO)


title: decidua

source_name: maternal endometrium, female

value: decidua


title: E1-KO_3_5

city: Philadelphia

first: Douglas

middle: J

last: Epstein

state: Pennsylvania

address: 415 Curie Blvd

department: Genetics

institute: University of Pennsylvania

description:
D867-1
KO-3

data_processing:
reads aligned to ribosomal sequences and repeats to remove these reads
data was aligned and expression values generated using RUM (Grant et al. 2011)
differential expression was determined using edgeR (Robinson et al., 2010)
Genome_build: mm10
Supplementary_files_format_and_content: .txt file of gene expression was generated by edgeR and presents expression levels, read counts and FPKM for each sample as well as comparison between control and Esrp1-/- expression. wig files were generated with RUM.

source_name: Embryonic Day 16.5 Cochlear Epithelium

extract_protocol:
whole E16.5 cochlear epithelium was extracted by manual dissection followed by treatment with collagenase P (0.1mg/ml) at 37oC for 15 min to remove surrounding mesenchyme, purified epithelium was then subject to RNA extraction in Trizol-LS with glycogen precipitation
NEBNext Ultra™ Directional RNA Library Prep Kit from Illumina

value: Cochlear Epithelium

tag: age

value: Embryonic day 16.5


title: QC_3


title: E1-KO_3_6

description:
D867-1
KO-3


title: Panc_DMSO_r1


title: E1-KO_2_4

description:
D501-1
KO-2


title: Panc_CH_r3

value: chaetocin (30nM)


title: E1-KO_1_2

description:
D593-1
KO-1


title: E1-KO_1_1

description:
D593-1
KO-1


title: Panc_CH_r2


title: Control3_6

description:
D867-7
WT-3

value: wild-type


title: Control2_3

description:
D501-7
WT-2


title: Panc_DMSO_r3


title: Control3_5

description:
D867-7
WT-3


title: Panc_CH_r1


title: Panc_CH+MLN_r3


title: Control1_2

description:
D593-5
WT-1


title: Control1_1

description:
D593-5
WT-1


title: HSC cd41low cd9low Gfi1 WT

city: Montreal

first: Möröy

last: Tarik

address: 110 Pine avenue West

institute: Insititut de Recherches Cliniques

data_processing:
RNA-Seq reads were aligned to mm10 using Tophat v2.0.10
Reads were processed with Samtools.
For differential expression, countfiles were generated by mapping reads to Ensembl genes using HTSeq. Further analysis was carried out using the DESeq R package
Genome_build: mm10
Supplementary_files_format_and_content: txt files are tab-delimited text files containing counts on Ensembl genes

source_name: Hematopoietic Stem Cells

extract_protocol:
Hematopoietic Stem Cells (Lin- cKit+ Sca1+ Cd48- CD150+) and Hematopoietic Stem Cells CD41low CD9low were sorted from mice tibiae, femora and humeri using a MoFlo cell sorter and RNA was extracted using a MagMax-96 Total RNA Isolation kit (Ambion).
RNA-Seq libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS.

value: tibiae, femora and humeri

value: Hematopoietic Stem Cells CD41low CD9low

tag: genotype/variation

value: Gfi1b WT


title: HSC cd41low cd9low Gfi1 KO

value: Gfi1b KO


title: HSC Gfi1 KO

value: Hematopoietic Stem Cells (Lin- cKit+ Sca1+ Cd48- CD150+)


title: HSC Gfi1 WT


title: HDLEC_siTie2_3

city: Irvine

first: Hosung

last: Bae

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer v.0.0.14), then mapped to hg19 whole genome using tophat2 v.2.0.9
Read count were calculated using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

growth_protocol: HDLECs were cultured in 60 mm dish until cells reach confluent state.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN mRNA-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: HDLECSs were incubated with 40 nM of siPROX1, siTIE2 or siControl for 24 hours, and harvested after 72 hours of siRNA treatment.

value: human dermal lymphatic endothelial cells (HDLECs)

value: Passage 6

tag: incubated with

value: 40 nM of siTIE2 for 24 hours

tag: time point

value: after 72 hours of siRNA treatment


title: HDLEC_siTie2_2


title: 9797_K_SP_MIEG3

city: Miami

first: Maria

middle: E

last: Figueroa

state: FL

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

description: DNMT3A-rescue control mouse #9797 ckit+ splenocytes

data_processing:
Reads were aligned against a bisulfite-converted version of the hg19 or mm10 builds of the genome using Bowtie followed by methylation percentage calling using Bismark (Krueger et al., 2011). Conversion rates were >99.8 for all samples. Only genomic regions with coverage between 10X and 500X were included for downstream data analysis.
ERRBS data analysis was performed using R statistical software version 3.0.3 and the MethylSig 0.1.3 package (Park et al., 2014) for differential methylation calling using the beta binomial method. The MethylKit 0.9.2.5 package (Akalin et al., 2012) was used for downstream gene-, CpG-, and enhancer region annotation analysis.
Differentially methylated regions (DMR) were identified by first summarizing the methylation status of genomic regions into 25-bp tiles and then identifying regions with absolute methylation difference ≥25% and false discovery rate (FDR) <10%. DMRs were annotated to GENCODE genes using a custom script with the following criteria: (i) DMRs overlapping with a gene were annotated to that gene, (ii) intergenic DMRs were annotated to all neighboring genes within a 50-kb window, and (iii) if no gene was detected within a 50-kb window, then the DMR was annotated to the nearest TSS (Meldi et al., 2015).
Genome_build: For murine ERRBS data, mm10 was used; for human ERRBS data, hg19 was used
Supplementary_files_format_and_content: tab-delimited text files

source_name: EV control Flt3ITD/ITD,Dnmt3afl/fl MxCre AML

growth_protocol: For murine ERRBS analyes: Mice were euthanized with carbon dioxide and cervical dislocation. Spleens were harvested from moribund Flt3ITD/ITD;Dnmt3afl/- MxCre and  Flt3ITD/ITD;Dnmt3afl/fl controls.  Splenocytes were isolated from freshly sacrificed mice and crushed between two glass slides. Red blood cells were lysed using Ammonium-Chloride-Potassium (ACK) buffer (Gibco), washed, and filtered to obtain single cells suspensions for downstream applications. For Human ERRBS analyses: bone marrow mononuclear cells from AML leukemia patients seen either at Erasmus Medical Center, Rotterdam or enrolled in the E1900 clinical trial from the Eastern Cooperative Oncology Group. All specimens consisted of >90% blasts. A total of 32 patients were included. Seventeen patients were FLT3-ITD/DNMT3A-wt while 13 patients were FLT3-ITD/DNMT3A-mut. All patients were wild-type for TET2, IDH1 and IDH2. Patients with FLT3-TKD were also excluded. Bone marrow mononuclear cells from 8 normal healthy donors were purchased from AllCells (Alameda, CA). Gene expression data for these patients had been previously published (Verhaak et al., 2009) (GEO accession number: GSE6891).

extract_protocol:
DNA was isolated from c-Kit+ splenocytes or single cell suspensions from CFU using the Qiagen Puregene kit according to manufacturer’s instructions. For small cell numbers glycogen was added to help precipitate DNA.
Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) libraries were generated from 25 ng of genomic DNA as previously described (Akalin et al., 2012) for the human specimens, and sequenced on a HiSeq-2000 sequencer. Murine libraries were prepared in the same way but using the indexed adaptors and sequenced with two libraries per lane on a HiSeq-2500 sequencer (Garrett-Bakelman et al., 2015).

treatment_protocol:
For Murine analyses: To isolated c-Kit+ leukemic stem/progenitor populations, freshly isolated single cells suspensions were incubated with CD117 MicroBeads and separated on an AutoMACS Pro separator (Miltenyi, San Diego, CA) according to manufacturer specifications. RNA was extracted from cKit+ purified splenocytes using TriZol (Invitrogen) according to manufacturers instructions. For Human analyses: bone marrow mononuclear cells from AML paitents were isolated perviously (Verhaak et al., 2009)
For DNMT3A rescue using murine AML in CFU experiments, MSCV-DNMT3A-GFP and empty vector MSCV-GFP retroviral plasmids were a kind gift from Dr. Grant Challen (Washington University, St. Louis). DNMT3A and EV retroviruses were used to transduce cKit+ leukemic splenocytes using the spinfection method. 48 hours post-transduction cells were sorted for GFP+ expression, and 2,000 cells were plated in methylcellulose M3434 supplemented in triplicate. After 7 days colonies were enumerated, single cell suspensions were made, and cells were mixed with cell lysis solution (Qiagen) (for DNA isolation).

value: cKit+ splenocytes

value: acute myeloid leukemia

tag: cytogenetics

tag: human dnmt3a

tag: human flt3itd

tag: human flt3tkd

tag: human idh1

tag: human idh2

tag: human tet2


title: HDLEC_siTie2_1

tag: cell line


title: 9301_K_SP_MIEG3

description: DNMT3A-rescue control mouse #9301 ckit+ splenocytes

tag: tissue

tag: cell type

tag: gender


title: 9797_K_SP_WT_DNMT

description: DNMT3A-rescue experiment mouse #9797 ckit+ splenocytes

source_name: DNMT3A-rescued Flt3ITD/ITD,Dnmt3afl/fl MxCre AML


title: 9301_K_SP_WT_DNMT

description: DNMT3A-rescue experiment mouse #9301 ckit+ splenocytes


title: 9798 Flt3ITD/ITD,Dnmt3afl/fl MPN

description: MPN control mouse #9798 ckit+ splenocytes

source_name: primary MPN

value: myeloproliferative neoplasm


title: 9927 Flt3ITD/ITD,Dnmt3afl/fl MPN

description: MPN control mouse #9927 ckit+ splenocytes


title: HDLEC_siProx1_3

value: 40 nM of siPROX1 for 24 hours


title: Control2_4

description:
D501-7
WT-2

tag: strain

value: Cochlear Epithelium

tag: genotype


title: Panc_CH+MLN_r2

tag: passage

tag: treatment


title: HDLEC_siProx1_2

tag: incubated with


title: RI-3 mRNA

first: Heng-Mu

last: Zhang

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by fastx_toolkit-0.0.13.2, then mapped to whole genome using SOAP with parameters: maximum number of mismatches allowed = 2bp， number of valid alignments per read pair (-k) = 40
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated.
Genome_build: http://rice.plantbiology.msu.edu/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: leaf cells

extract_protocol:
Tissue samples were stored at -80°C prior to use, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Infected leaf cells


title: RI-2 mRNA


title: E1-KO_2_3

description:
D501-1
KO-2

tag: age

value: Embryonic day 16.5


title: Panc_CH+MLN_r1


title: 8303 Flt3ITD/ITD,Dnmt3afl/- MxCre AML

description: AML experimental mouse #8303 ckit+ splenocytes

source_name: primary AML

tag: cytogenetics


title: 9301 Flt3ITD/ITD,Dnmt3afl/- MxCre AML

description: AML experimental mouse #9301 ckit+ splenocytes

tag: human dnmt3a


title: RI-1 mRNA


title: HDLEC_Con_3

value: 40 nM of siControl for 24 hours

tag: time point


title: HDLEC_Con_2


title: Chlamydomonas reinhardtii, replicate 3 (4A+, log phase)

city: Walnut Creek

first: Denis

last: Tolkunov

address: 2800 Mitchell Dr

institute: DOE Joint Genome Institute

data_processing:
Adaptors were trimmed, the paired reads were aligned to the reference genome by BSMAP.
Genome_build: C.Reinhardtii_236 (JGI Phytozome assembly V5.0)
Supplementary_files_format_and_content: bigWig file

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii, replicate (4A+, log phase) _Whole organism

extract_protocol:
C. reinhardtii wild type strain 4a+ were cultured using Tris-acetate-phosphate (TAP) medium in Erlenmeyer flasks at 25 degrees Celsius with agitation at 180 rpm under light irradiation at 100 microE. Cells were harvested at mid-log phase (at approximately 2 x 106 cells/ml). Cells were lysed using lysis buffer (50mM Tris-HCl pH 8, 200mM NaCl, 2mM EDTA, 2% SDS and proteinase K) and genomic DNA was extracted using CTAB-based protocol39.
5ug of gDNA was sheared to 700bp using the focused-ultrasonicator S2 (Covaris) and spiked in with 50ng HaeIII digested lambda DNA for quality control. The fragments were treated with end-repair, A- tailing, and ligation of methylated Illumina adaptors (Illumina) using the DNA library preparation kit for Illumina (Kapa Biosystems). The adaptor ligated DNA was subjected to bisulfite treatment using EpiTect Bisulfite Kit (Qiagen). The bisulfite-treated DNA was amplified with 8 cycles of PCR with uracil-insensitive Taq polymerase (Pfu Turbo Cx Hotstart DNA polymerase; Stratagene). The PCR product was run on a 2% agarose gel followed by gel excision to select for fragments between 300 to 400bp. Purified library was sequenced on the Illumina Hiseq.

tag: growth phase

value: log phase


title: AR ChIPSeq_abl_GSK treated

city: San Antonio

first: Kexin

last: Xu

state: TX

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
FASTQ files were mapped to hg19 (Homo Sapiens) and dm3 (Drosophila melanogaster) assemblies respectively using BOWTIE (version 0.12.7); duplicated reads were removed.
ChIP-Seq peaks and bigwig files were called and generated using MACS2 (version 2.1.0)
Genome_build: hg19 (human) and dm3 (drosophila)
Supplementary_files_format_and_content: BED files, containging the location of the peaks
Supplementary_files_format_and_content: BigWig files, containing the enrichment information

source_name: abl_GSK treated

growth_protocol: Both DU145 and LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI1640 with 10% charcoal-stripped FBS plus 1% Penicillin-Streptomycin.

extract_protocol:
Prostate cancer cells were crosslinked with 1% formaldehyde and lysed in RIPA buffer with 0.3 M NaCl. ChIP DNA was purified using PCR Purification Kit (Qiagen) and then quantified by Quant-iTTM dsDNA HS Assay Kit (Invitrogen).
ChIP-Seq libraries were prepared using ThruPLEX-FD Prep Kit (Rubicon Genomics) according to the manufacturer's protocol.

treatment_protocol: Both types of cells were treated with vehicle (DMSO), GSK126 or EPZ-6438 at final concentrations of 5 uM for 4-5 days before the cells were crosslinked and collected.

value: LNCaP-abl (abl)

tag: cell types

value: castration resitant prostate cancer cells

tag: cell phenotype

value: AR-positive, EZH2 inhibitor-sensitive

tag: passages

tag: treated with

tag: chip antibody

value: AR Antibody (H-280) (Santa Cruz, sc-13062)


title: PN_ko_sham

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

data_processing:
Illumina Casava v1.7 used for basecalling.
Sequences were mapped to mm10 using TopHat v2.03 and Bowtie 2.0.0.6 with parameters -m 1 -n 2 --library-type fr-unstranded
FPKM values were computed using cuffdiff 2.01 with parameters -u  -q --library-type fr-unstranded --total-hits-norm --geometric-norm
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including FPKM values for all genes showing lack of response in PTZ treated Tau -/- mice

source_name: Brain

growth_protocol: Primary neurons obtained from tau+/+ and tau-/- neurons were cultured as previously described (Fath, 2009).

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: At 6 weeks of age, mice were injected intraperitoneally with 50mg/kg bodyweight of pentylenetrazole.

value: 6 weeks

value: Tau -/-

value: sham


title: PN_wt_treat

value: Tau +/+

value: PTZ


title: PN_ko_treat


title: mel rep7

description:
Sample 7
single-cell transcriptomics

source_name: Drop-seq of whole embryo

extract_protocol:
Embryos were dissociated first in a Dounce homogenizer and then further using a syringe with 22G x 2" needle, followed by filtering through 20 um cell strainer and fixation in 80% methanol/PBS
Captured transcriptomes were reverse transcribed while bound on barcoded oligo dT beads; PCR handles added by template switching; cDNA PCR-amplified (4 + 9 cycles); 600 pg cDNA library fragmented and amplified with Nextera XT v2 DNA sample preparation kit using custom primers for 3'-targeted amplification (Macosko et al. 2015 Cell 161)
Drop-seq single-cell transcriptome profiling according to Macosko et al. 2015 Cell 161

tag: developmental stage

value: stage 6

tag: cell type

value: dissociated cells

value: D.mel y1 w1118 ; P{st.2::Gal4} ; P{vnd::dsRED}

tag: fixation

value: 80% methanol/PBS


title: AR ChIPSeq_abl_DMSO treated

source_name: abl_DMSO treated

tag: cell line

value: vehicle (DMSO)


title: 9796 Flt3ITD/ITD,Dnmt3afl/fl MPN

description: MPN control mouse #9796 ckit+ splenocytes

tag: tissue

value: cKit+ splenocytes

value: myeloproliferative neoplasm

tag: gender

tag: human flt3itd

tag: human flt3tkd

tag: human idh1

tag: human idh2

tag: human tet2


title: mel rep6

description:
Sample 6
single-cell transcriptomics

tag: strain


title: PN_wt_sham

tag: age

tag: genotype

tag: treatment


title: mel rep5

description:
Sample 5
single-cell transcriptomics


title: AR ChIPSeq_abl_EPZ treated

source_name: abl_EPZ treated

tag: cell types

tag: cell phenotype

tag: passages

tag: treated with


title: mel rep4

description:
Sample 4
single-cell transcriptomics

tag: developmental stage

tag: cell type

tag: fixation


title: H358_ChIPseq_H3K27me3

first: Bin

last: Xiang

address: Building 3, 4218 Jinke Road, Pudong

institute: novartis institutes for biomedical research

data_processing:
The ChIP-seq was conducted in the human lung cancer cell line H358 cells using FXR1 and several histone H3 methylation specific antibodies on the platform Illumina HiSeq 2000.
ChIP-seq data quality was analyzed using FastQC. FXR1 or histone mark binding genomic regions (called ChIP-seq peaks) were identified by Model-based Analysis of ChIP-Seq (MACS) algorithm using the default p-value cutoff of 1e-5.
Reads in the fastq file were trimmed by 5 base pairs in the 5´-end, and then mapped to the reference human genome (HG19) with the algorithm Burrows-Wheeler Aligner (BWA). The mapped reads were filtered with BamTools using criteria that the mapping quality should be >= 30.
The distribution of FXR1 ChIP-seq peaks were investigated by the annotations on the human genome. The peaks were binned into three groups according to the positions relative to annotated genes: promoter, gene body, and intergenic region. The aggregation signals of FXR1, H3K4me3, H3K9me3 and H3K27me3 across the whole genome were plotted using the ceasBW tool.
A hub for UCSC genome browser was constructed in order to investigate the detailed information of the peaks. The summit positions of the FXR1 ChIP-seq peaks were extended to 50 bp both up- and down-stream by MACS to construct the BED files. After converting the BED files into FASTA files using the reference genome sequence, the BED files were provided to MEME.
Genome_build: HG19
Supplementary_files_format_and_content: *peaks.txt file is the original peak calling result. FXR1 or histone mark binding genomic regions (called ChIP-seq peaks) were identified by Model-based Analysis of ChIP-Seq (MACS) algorithm using the default p-value cutoff of 1e-5.
*genepeak.txt file shows the peaks with gene annotation. The distribution of FXR1 or histone mark ChIP-seq peaks were investigated by the annotations on the human genome.
*filter.bw file shows the aggregation signals of FXR1 or histone mark across the whole genome which were plotted using the ceasBW tool.
ChIP-seq-DAVID.FXR1.BindGene.Up5k.xlsx describes the function clustering of the genes with FXR1 ChIP-seq peaks at their 5kb upstream region using the DAVID (The Database for Annotation, Visualization and Integrated Discovery) analysis.
ChIP-seq-FXR1+H3K4me3 peaks.xlsx' belongs to the H358_ChIPseq_FXR1 sample and the H358_ChIPseq_H3K4me3 sample, which comparing the FXR1 ChIP-seq peaks and the H3K4me3 ChIP-seq peaks.
ChIP-seq-FXR1.RegioSumma.xlsx shows the region of the peaks: the peaks were binned into three groups according to the positions relative to annotated genes: promoter, gene body, and intergenic region.

source_name: Human non small cell lung cancer cell line

growth_protocol: Human lung cancer cell line H358 and gastric carcinoma cell line KATOIII were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS, GIBCO) and 100 U/mL penicillin-streptomycin (GIBCO) in humidified incubator set at 37°C with 5% CO2 using the standard techniques

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

tag: chip antibody

value: anti-H3K27me3 (Millipore, 07-449)


title: mel rep3

description:
Sample 3
single-cell transcriptomics


title: HDLEC_siProx1_1

value: human dermal lymphatic endothelial cells (HDLECs)

tag: passage

value: Passage 6

tag: incubated with

value: 40 nM of siPROX1 for 24 hours

tag: time point

value: after 72 hours of siRNA treatment


title: 9797 Flt3ITD/ITD,Dnmt3afl/- MxCre AML

description: AML experimental mouse #9797 ckit+ splenocytes

tag: tissue

value: acute myeloid leukemia

tag: gender

tag: cytogenetics

tag: human dnmt3a

tag: human flt3itd

tag: human flt3tkd

tag: human idh1

tag: human idh2

tag: human tet2


title: H358_ChIPseq_H3K9me3

value: Human non small cell lung cancer cell line

value: anti-H3K9me3 (Active Motif, 39161)


title: H358_ChIPseq_H3K4me3

value: anti-H3K4me3 (Cell Signaling Technology, 9727)


title: 45213 HSC

description: Normal healthy donor hematopoietic stem cells

source_name: normal healthy donor

value: bone marrow hematopoietic stem cell

value: normal bone marrow

tag: age


title: H358_ChIPseq_FXR1

tag: cell type

value: anti-FXR1 (Sigma, HPA018246)


title: 45211 HSC


title: 45207 HSC


title: 45205 HSC


title: 7421 Flt3ITD/ITD,DNMT3Awt

description: AML patient bone marrow mononuclear cells

value: bone marrow mononuclear cells

value: male

value: normal

value: wild type

value: mutation


title: HDLEC_Con_1

value: 40 nM of siControl for 24 hours


title: 7176 Flt3ITD/ITD,DNMT3Awt


title: mel bulk

description:
Sample 8
bulk transcriptomics

source_name: mRNAseq of whole embryo

extract_protocol:
Whole, live embryos were dissolved in TRIZOL, shock-frozen in liquid nitrogen, then total RNA was extracted
Libraries were generated from 200 ng RNA with NEBNext Ultra RNA Library Prep Kit for Illumina using poly(A) mRNA magnetic isolation.
mRNAseq, unstranded

tag: developmental stage

value: stage 6

value: intact embryo

tag: strain

value: D.mel y1 w1118 ; P{st.2::Gal4} ; P{vnd::dsRED}

tag: fixation

value: live, not fixed


title: 7052 Flt3ITD/ITD,DNMT3Awt

value: acute myeloid leukemia

value: female

value: Other


title: 7051 Flt3ITD/ITD,DNMT3Awt


title: SOD1 D90A rep 2 (Hs)

city: Edinburgh

first: Christopher

last: Sibley

address: 1 George Square

institute: University of Edinburgh

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using fastx_clipper and converted to reverse complement with fastx_reverse_complement (both fastx_toolkit v0.0.14)
Reads were mapped to hg19 with annotation Homo_sapiens.GRCh37.75 using tophat2 (v2.0.11)
Reads were sorted and indexed using samtools (v0.1.19)
Sorted sam files were used as input to ht-seq count against Homo_sapiens.GRCh37.75
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each Sample ...

source_name: SOD1 D90A, iPSC derived astrocytes

growth_protocol: Patterned iPSC-derived neural precursor cells were propagated for >60 days with 10ng/ml FGF-2, then terminally differentiated to astrocyes in presence of BMP4 (10ng/ml) and LIF (10ng/ml)

extract_protocol:
RNeasy plus mini kit (Qiagen)
Illumina TruSeq RNA Access library preparation kit

treatment_protocol: Untreated

tag: mutation

value: SOD1 D90A

value: iPSC derived astrocytes

tag: genotype/variation

value: SOD1 D90A mutation


title: SOD1 D90A rep 1 (Hs)


title: 6379 Flt3ITD/ITD,DNMT3Awt


title: 6237 Flt3ITD/ITD,DNMT3Awt


title: SOD1 D90A rep 3 (Hs)


title: 6463 Flt3ITD/ITD,DNMT3Awt


title: 5287 Flt3ITD/ITD,DNMT3Awt


title: 2327 Flt3ITD/ITD,DNMT3Awt


title: H358_ChIPseq_Input

city: Shanghai

tag: cell line

value: Human non small cell lung cancer cell line

tag: chip antibody

value: none (Input)


title: 293FLP_SETBP1_Empty_V5_hg19_rmdup.bigwig

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Alignment to the hg19 reference genome was performed with TopHat 2.1.1
Peak calling was performed with MACS2 v2.1
Genome_build: hg19
Supplementary_files_format_and_content: bigwig coverage files have been generated with bedtools 2.18

source_name: HEK 293FLP

extract_protocol:
DNA has been isolated with the PureLink Genomic DNA kit (Thermo Fisher Scientific), according to manufacturer's instructions.
Libraries have been build with the TruSeq ChIP Library Prep Kit, according to manufacturer's instructions.

tag: vector cds

value: Empty V5

tag: antibody

value: Anti-V5 Agarose Affinity Gel antibody, clone V5-10

tag: antibody vendor

value: Sigma

tag: antibody catalog


title: 293FLP_SETBP1_G870S_hg19_rmdup.bigwig

value: SETBP1 G870S


title: SETBP1_G870SSETBP1_G870S∆HCF1_2

data_processing:
Base calling …
Alignment to the hg38 reference genome was performed with Spliced Transcripts Alignment to a Reference (STAR) v2.5
Genome_build: hg38
Supplementary_files_format_and_content: gene count calculations were performed with Spliced Transcripts Alignment to a Reference (STAR) v2.5

extract_protocol:
Total RNA has been isolated with the TRIzol® RNA Isolation Reagent (Thermo Fisher Scientific), according to manufacturer's instructions.
Stranded libraries will be prepared from 2 µg of total RNA in accordance with the TruSeq RNA sample preparation guide (Illumina).


title: SETBP1_G870SSETBP1_G870S∆HCF1_1


title: 45209 HSC

tag: tissue

value: bone marrow hematopoietic stem cell

value: normal bone marrow

tag: gender

tag: cytogenetics

tag: human dnmt3a

tag: human flt3itd

tag: human flt3tkd


title: SETBP1_G870SSETBP1_G870S∆HCF1_3


title: 2248 Flt3ITD/ITD,DNMT3Awt

value: bone marrow mononuclear cells

tag: cell type

tag: age

value: normal

value: wild type

value: mutation

tag: human idh1

tag: human idh2

tag: human tet2


title: SETBP1_G870SSETBP1_G870S_3

tag: genotype/variation


title: Bl-2

city: Davis

first: Pablo

middle: Juan

last: Ross

address: 1 Shields Ave, 2239 Meyer Hall

department: Animal Science

institute: University of California Davis

description: Processed file_RPKM_all_samples.csv

data_processing:
Filtering for quality (q>0.05) and trimmed off 10 bp from 5" end using CLC Genomics Workbench Ver. 6.0.2
RNA-Seq analysis using CLC Genomics Workbench Ver. 6.0.2
RhesusBase gene annotation
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: Processed file_RPKM_all_samples.csv contains RPKM  in comma separated value format (.csv)

organism: Macaca mulatta

source_name: Blastocyst stage embryo

extract_protocol:
Whole cell lysate
Clonetech SMARTer Ultra Low Input RNA kit for Illumina Sequencing
Illumina TruSeq DNA library preparation kit

tag: sample type

value: single embryo

tag: source

value: Derived after intacytoplasmic sperm injection and in vitro embryo culture

tag: Stage

value: Blastocyst stage


title: 2236 Flt3ITD/ITD,DNMT3Awt

value: acute myeloid leukemia

value: female


title: SETBP1_G870SSETBP1_G870S_2


title: 2301 Flt3ITD/ITD,DNMT3Awt

value: male


title: 2230 Flt3ITD/ITD,DNMT3Awt


title: Mo-3

description: Processed file_RPKM_all_samples.csv

source_name: Morula stage embryo

value: Morula stage


title: 2197 Flt3ITD/ITD,DNMT3Awt


title: Bl-1

description: Processed file_RPKM_all_samples.csv


title: SETBP1_G870SSETBP1_G870S_1


title: SETBP1_G870SEmpty3

value: WT


title: 2179 Flt3ITD/ITD,DNMT3Awt


title: SETBP1_G870SEmpty2


title: SETBP1_G870SEmpty1


title: 293FLP_SETBP1_WT_hg19_rmdup.bigwig

tag: vector cds

value: SETBP1 WT

tag: antibody

value: Anti-V5 Agarose Affinity Gel antibody, clone V5-10

tag: antibody vendor


title: Mo-1

description: Processed file_RPKM_all_samples.csv


title: 322 Flt3ITD/ITD,DNMT3Awt

tag: tissue

tag: gender

value: Other


title: 20599 Flt3ITD/ITD,DNMT3Amut

tag: cytogenetics

tag: human dnmt3a


title: 8C-1

description: Processed file_RPKM_all_samples.csv

source_name: Eight-cell stage embryo

value: Eight-cell stage


title: 4C-3

description: Processed file_RPKM_all_samples.csv

source_name: Four-cell stage embryo

value: Four-cell stage


title: 4C-2

description: Processed file_RPKM_all_samples.csv


title: 19274 Flt3ITD/ITD,DNMT3Amut

value: bone marrow mononuclear cells

value: NKL

tag: human flt3itd

tag: human flt3tkd


title: SETBP1_G870S H3K4me2

data_processing:
Alignment to the hg19 reference genome was performed with TopHat 2.1.1
Histone mark abundance was performed with deepTools2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig coverage files have been generated with bedtools 2.18

value: Diagenode

tag: antibody catalog


title: SETBP1_G870S H3K4me3

value: abcam


title: SETBP1_G870S H3K36me3


title: 14707 Flt3ITD/ITD,DNMT3Amut

tag: cell type

tag: age

value: not done

value: mutation

value: wild type

tag: human idh1


title: SETBP1_G870S H3K9Ac

tag: genotype/variation

value: Active Motif


title: 4C-1

description: Processed file_RPKM_all_samples.csv

tag: sample type

value: single embryo

value: Derived after intacytoplasmic sperm injection and in vitro embryo culture


title: 19694 Flt3ITD/ITD,DNMT3Amut

value: acute myeloid leukemia

value: female

tag: human idh2

tag: human tet2


title: SETBP1_G870S H3K27Ac


title: Empty H3K9Ac

value: WT


title: 2C-1

description: Processed file_RPKM_all_samples.csv

source_name: Two-cell stage embryo

tag: source

tag: Stage

value: Two-cell stage


title: PN-3

description: Processed file_RPKM_all_samples.csv

source_name: Pronuclear stage embryo

value: Pronuclear stage


title: 2C-2

description: Processed file_RPKM_all_samples.csv


title: Empty H3K4me3

tag: antibody

tag: antibody vendor


title: Mo-2

description: Processed file_RPKM_all_samples.csv

value: Morula stage


title: 7411 Flt3ITD/ITD,DNMT3Amut

source_name: primary AML

tag: tissue

tag: gender

value: normal


title: 7131 Flt3ITD/ITD,DNMT3Amut

value: bone marrow mononuclear cells

tag: cytogenetics

value: failure

tag: human dnmt3a


title: 8C-2

description: Processed file_RPKM_all_samples.csv

value: Eight-cell stage


title: PN-2

description: Processed file_RPKM_all_samples.csv


title: 6374 Flt3ITD/ITD,DNMT3Amut

value: male

tag: human flt3itd

tag: human flt3tkd


title: OGCT8

city: Stockholm

first: Roger

middle: Kae-Jia

last: Chang

address: Karolinska Univ Hospital, R8:04

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Adapter sequences were removed, and sequences were filtered using the package Fastx-toolkit
The resultant dataset were aligned to miRBase database version 21 for human mature miRNA using Bowtie short read aligner with settings -f -n 0 -l 15 -k 200 -S –best –chunkmbs 128
Reads were sorted and indexed by SAMtools
For miRNA quantification, the script HTSeq-count of the HTSeq was used
Supplementary_files_format_and_content: txt files, mapped reads to human mature miRNA sequences

extract_protocol:
mirVana miRNA isolation kit (Applied Biosystems/ Ambion, Austin, TX) was used to extract small RNA
for cloning small RNAs were ligated with adenylated 3’-adaptor oligonucleotide [/5rApp/CTGTAGGCACCATCAAT/3ddC; IDT Inc., Coralville, IA, USA] and purified on a 12% denaturing polyacrylamide gel. Second ligation reaction was performed with 5’-adaptor oligonucleotide [5'-ACGCTCTTCCGATCTv-3' (uppercase, DNA; v = barcodes with triple RNA molecules: aaa, ggg, ccc or uuu; IDT)], followed by gel purification. The double ligated product was converted to cDNA using the reverse transcription enzyme SuperScript II (Invitrogen) and the reverse primer [5'-ATTGATGGTGCCTACAG-3'], and then PCR amplified for 16-20 cycles using a forward primer 5'-GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3' and a reverse primer 5'-CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC TAT TGA TGG TGC CTA CAG- 3'.

value: ovarian germ cell tumor

tag: diagnosis

value: benign

tag: histology

value: mature teratoma

tag: patient age

value: 51 year-old


title: OGCT6

value: 77 year-old


title: Empty H3K36me3

tag: genotype/variation

value: abcam

tag: antibody catalog


title: OGCT7

value: 47 year-old


title: PN-1

description: Processed file_RPKM_all_samples.csv

tag: sample type

value: single embryo

value: Derived after intacytoplasmic sperm injection and in vitro embryo culture


title: 15492 Flt3ITD/ITD,DNMT3Amut

tag: cell type

value: acute myeloid leukemia

tag: age

value: female

value: mutation

value: wild type

tag: human idh1

tag: human idh2

tag: human tet2


title: Empty H3K4me2

value: WT

tag: antibody

tag: antibody vendor

value: Diagenode


title: 5286 Flt3ITD/ITD,DNMT3Amut

tag: tissue

value: bone marrow mononuclear cells

tag: gender

tag: cytogenetics

value: normal


title: Empty H3K27Ac


title: OGCT5

value: ovarian germ cell tumor


title: MII-3

description: Processed file_RPKM_all_samples.csv

source_name: Metaphase II stage oocyte

value: single oocyte

tag: source

value: Collected post-mortem from superovulated donor

tag: Stage

value: Metaphase II stage


title: OGCT4

tag: diagnosis

value: benign

tag: histology

value: mature teratoma

value: 64 year-old


title: MII-2

description: Processed file_RPKM_all_samples.csv


title: MI-2

description: Processed file_RPKM_all_samples.csv

source_name: Metaphase I stage oocyte

value: Metaphase I stage


title: MI-1

description: Processed file_RPKM_all_samples.csv


title: SCST3

value: sex cord-stromal tumor

value: malignant

tag: patient age

value: 46 year-old


title: MII-1

description: Processed file_RPKM_all_samples.csv


title: SR-0788-siKPC1_R2

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
Base calling and demultiplexing were processed using CASAVA version 1.8
Reads were mapped using the GENCODE release 19 reference using STAR version 2.4.2a
Read counts were generated using the quantMode GeneCounts option in STAR.
Fold change differences between samples were detected using the GFOLD version 1.1.4 algorithm.
Genome_build: GENCODE release 19 (GRCh37.p13)
Supplementary_files_format_and_content: tab files contain read counts and csv file contains gfold output. Columns for the tab files are as follows: 1) gene id 2) counts for unstranded RNA-seq, 3) counts for the 1st read strand aligned with RNA (htseq-count option -s yes) and 4) counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse).

source_name: malignant melanoma

extract_protocol:
Total RNA was extracted Direct-zol RNA MiniPrep kit (Zymo Research).
mRNA libraries were constructed using Illumina TruSeq RNA Sample Preparation kit v2.

tag: cell line

tag: transfected sirna


title: SR-0788-siCntl_R2

value: Control


title: SR-0788-siCntl_R1


title: SR-0788-siKPC1_R1


title: 6239 Flt3ITD/ITD,DNMT3Amut

tag: cell type

value: acute myeloid leukemia

value: female

tag: human dnmt3a

value: mutation

tag: human flt3itd

tag: human flt3tkd

value: wild type


title: SCST2

value: fibrothecoma

value: 45 year-old


title: 2195 Flt3ITD/ITD,DNMT3Amut

value: bone marrow mononuclear cells

tag: age

value: male

value: normal

tag: human idh1

tag: human idh2

tag: human tet2


title: WC00060-siCntl_R2


title: WC00060-siKPC1_R1


title: GV-1

description: Processed file_RPKM_all_samples.csv

source_name: Germinal Vesicle stage oocyte

tag: sample type

value: single oocyte

value: Collected post-mortem from superovulated donor

value: Germinal Vesicle stage


title: goat mammary gland from lactation period (R) RNA-Seq data

city: Chengdu

first: Jiangjiang

last: Zhu

state: Sichuan

address: #16, South Section, 1st Ring Road

department: Institute of Qinghai-Tibetan Plateau

institute: Southwest Uniersity for Nationalities

data_processing:
The raw reads were first determined by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and filtered by removing potential contamination, i.e. reads with unknown base more than 1 N (base not available), and low quality sequences (<Q30). By aligning the sequences with a goat database constructed previously (BioProject ID: PRJNA243005), the unigene expression level was recorded according to the sum frequencies of compared reads. Reads per kilo base of exon model per million mapped reads (RPKM) was used for expression normalization. Unigene annotation, GO annotation, KOG classification and KEGG analysis were performed according to our previous study.
Genome_build: PRJNA243005
Supplementary_files_format_and_content: excel file with expression data.

organism: Capra hircus

source_name: lactation period (R)

extract_protocol:
Total RNA extraction, mRNA purification, and cDNA library construction were conducted by LC Sciences (Houston, TX, USA). In brief, total RNA was obtained from mammary tissue using the total RNA purification kit (LC Sciences, Houston, TX, USA) as instructed, treated with RNAase free DNAase, and re-purified with the RNA easy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA).
mRNA was isolated with poly-T-oligo-attached magnetic beads (Invitrogen, USA). Following purification, the mRNA was fragmented into small pieces using divalent cations at high temperature. After phosphatase and PNK treatment, the cleaved RNA fragments were reverse-transcribed and purified the 200-300bp fragments using 6% polyacrylamide Tris-borate-EDTA to create the final cDNA library. One end sequencing of 1×36bp was then performed on an Illumina HiSeq 2000 equipment following the vendor’s recommended protocol.

tag: tissue

value: mammary gland

tag: breed

value: Xinong Saanen

tag: age/developmental stage

value: 100 days postpartum


title: SCST1

value: sex cord-stromal tumor

tag: diagnosis

value: benign

value: signet ring stromal tumor

value: 84 year-old

tag: gender


title: goat mammary gland from lactation period (R) RNA-Seq data rep 2


title: WC00060-siCntl_R1

value: Control


title: wild-type (Col-0)

city: Athens

first: Polydefkis

last: Hatzopoulos

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

data_processing:
Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10).
Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10).  RNA-seq data were analyzed using the SOAPnuke (version v.1.5.2) with parameters “-l 15 -q 0.2 -n 0.05” and the HISAT2 pipeline (version 2.0.4) with parameters “--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000”
Differential alternative splicing events were detected for lefko1 and wild-type using rMATS.
genome build: Arabidopsis genome reference (TAIR10)
processed data files format and content: Excel file with alternative splicing enents (Intron retention, 5’ and 3’ alternative start site, exon skipping) including Gene ID and coordinates.

organism: Arabidopsis thaliana

source_name: Arabidopsis seeds

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized and sown in Petri dishes containing 0.5x Murashige and Skoog (MS) medium (Duchefa) pH 5.7, supplemented with 1% sucrose and solidified with 0.4% phytagel (Sigma). After 24 hr of stratification at 4°C, seedlings were positioned to grow vertically after germination at 22°C in a Fitotron growth chamber under a long photoperiod with 16h of light and 8h of darkness per day and 100 μmol m–2 s–1 light intensity. Seedlings transferred to pots to grow until maturity.

extract_protocol:
Globular to heart stage lefko2 mutant and wild-type Arabidopsis embryos were dissected from siliques. Total RNA was extracted using the NucleoSpin Plant RNA kit (Macherey-Nagel, Düren, Germany) with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of the RNA were assessed using a NanoDrop 1000 spectrophotometer and agarose gel electrophoresis.
RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina).

tag: ecotype

tag: genotype/variation

value: wild type


title: goat mammary gland from lactation period (R) RNA-Seq data rep 1


title: 3331 Flt3ITD/ITD,DNMT3Amut

value: acute myeloid leukemia

value: female

tag: cytogenetics

value: mutation


title: lefko1


title: goat mammary gland from dry-off (G) RNA-Seq data

source_name: dry-off (G)

value: 310 days postpartum


title: 2185 Flt3ITD/ITD,DNMT3Amut

value: bone marrow mononuclear cells

tag: cell type

value: normal


title: goat mammary gland from dry-off (G) RNA-Seq data rep1


title: H3K4me3_ChIPSeq_rep2

city: Kweishan, Taoyuan

first: Shu Yuan

last: Yang

address: Wenhua 1st Rd, No. 259

country: Taiwan

institute: Chang Gung University

data_processing:
Fastq files were applied to Fastqc to ensure quality control.
Fastq files were mapped to the D. melanogaster genome using bowtie with default parameters.
Mapped reads were converted to BAM files using SAMTOOLS.
Peaks were called using MACS at MFOLD (3, 30) and p=1x10^(-3).
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: wig files were generated using MACS.

source_name: Testes, bam-, H3K4me3 ChIP

growth_protocol: Fruit flies were grown at 25⁰C on standard medium.

extract_protocol:
Testes were dissected in cold PBS, fixed, sonicated, and clarified lysates were used for ChIP with specific antibodies.
Libraries were prepared with the NEXTflex ChIPseq Kit (Bioo Scientific) according to manufacturer's suggestions.

value: bam-

value: Testis

value: Within 3 days of eclosion

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: WC00060-siKPC1_R2

tag: cell line

tag: transfected sirna


title: H3K4me3_input_rep2

source_name: Testes, bam-, input

tag: age


title: H3K4me3_input_rep1


title: GV-2

description: Processed file_RPKM_all_samples.csv

value: single oocyte

tag: source

value: Collected post-mortem from superovulated donor

tag: Stage

value: Germinal Vesicle stage


title: goat mammary gland from non-lactation period (K) RNA-Seq data rep1

source_name: non-lactation period (K)

value: mammary gland

value: Xinong Saanen

value: non-lactation and non-pregnant period


title: goat mammary gland from non-lactation period (K) RNA-Seq data


title: H3K4me2_input_rep2


title: H3K4me2_ChIPSeq_rep2

source_name: Testes, bam-, H3K4me2 ChIP

value: H3K4me2 (Abcam, Y47)


title: H3K4me2_input_rep1


title: H3K4me2_ChIPSeq_rep1


title: Phf7-bam- rep2

description: oligo-dT selected RNA

data_processing:
The Fastq files were converted to Sanger Fastq files using Fastq Groomer on the Galaxy platform.
The RNAseq reads were mapped to the Drosophila genome (dm3) with Tophat2 on the Galaxy platform using default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks on the Galaxy platform using default parameters.
Genes with significant expression differences between the two genotypes were determined with Cuffdiff on the Galaxy platform using 0.05 as the false discovery rate.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *.tabular.txt: Tab-delimited text files include RPKM values for each sample.

source_name: Testis, Phf7-bam-

extract_protocol:
Testes were dissected into cold PBS, extracted with RNABee (TelTest), and selected with oligo-dT beads (Thermo Fisher Scientific).
RNA libraries were prepared with the NEXTflex Directional RNAseq Kit (Bioo Scientific).


title: goat mammary gland from non-lactation period (K) RNA-Seq data rep2


title: bam rep1

description: oligo-dT selected RNA

source_name: Testis, bam-


title: H3K4me3_ChIPSeq_rep1


title: TCP

first: Wei

last: Liu

address: Wangjiang Road 29

department: college of life sciences

institute: Sichuan university

description: 13-41 nt small RNAs

data_processing:
The adaptor sequences in raw reads and low quality reads were removed using FASTX-Toolkit V0.0.13.
The small RNA reads with length of 13-40 nt were mapped to the genome (MSU 7) and previously predicted tRNA gene using bowtie V1.1.2  with parameters -f -m 1 -t --best --strata.
Genome_build: MSU7
Supplementary_files_format_and_content: counts

source_name: Rice tricellular pollen

growth_protocol: Rice grown under Southwest China's natural field conditions

extract_protocol:
Extraction of total RNA was performed using MiR VanaTM RNA Isolation Kit (Ambion), according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tissue samples were collected at sunny noon on July. Collected biological samples were frozen in liquid nitrogen and kept -80 ℃ until RNA extraction.

tag: cultivar

value: Guichao No.2

value: pollen

tag: developmental stage

value: tricellular pollen


title: Tobacco_TYLCCNV infected

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

institute: Zhejiang University

description: 25 days post-inoculation

data_processing: The adapter-ligated tags are fixed on the Solexa Sequencing Chip to form single-molecule cluster, and then sequencing by synthesis is performed to generate millions of raw data with sequencing length of 35bp. Raw sequences were transformed into clean tags through removing adaptor sequence, low quality sequences. For annotation, all tags were mapped to the reference sequences and only allowed no more than 1 nucleotide mismatch. For gene expression analysis, the number of unambiguous clean tags for each gene was calculated and then normalized to TPM.

organism: Nicotiana tabacum

source_name: Tobacco leaves

growth_protocol: Clones of TYLCCNV with its satellite DNA, also known as DNA-beta, were used as inocula. To obtain virus-infected tobacco, plants at the 3-4 true-leaf stage were inoculated with TYLCCNV and its DNA-beta by agroinoculation. The control tobacco plants were mock inoculated using the same Agrobacterium strain. TYLCCNV inoculated and mock inoculated tobacco plants were cultivated to the 6-7 true-leaf stage at 22 days post-inoculation.

extract_protocol: Total RNA was isolated using the SV total RNA isolation system (Promega) according to the manufacturerâs protocol. We constructed the library for the above four samples according to Illumina's instructions.

treatment_protocol: Six tobacco plants were used in each treatment. For the whitefly feeding treatment, approximately 6,000 adult whiteflies that emerged from the tobacco plants were allowed to distribute randomly onto the leaves of six mock inoculated plants in one cage, and 6,000 adult whiteflies that emerged from the tobacco plants were released onto the leaves of six virus infected plants in another cage. After 72 h of feeding, all the adult whiteflies were discarded. Then the comparable leaves from the six plants in each of four treatments were harvested, flash-frozen in liquid N2 and stored at -80 °C.

tag: tissue

value: leaves

tag: inocula

value: TYLCCNV


title: Auricularia delicata (TFB10046 SS-5)

data_processing:
SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: A.delicata_TFB10046_SS_5_mjb_082712 (JGI Mycocosm A. subglabra V2.0)
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference.  The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files

organism: Auricularia delicata

source_name: Auricularia delicata (TFB10046 SS-5) _Whole organism

extract_protocol:
Auricularia delicata, strain TFB10046, SS-5 was prepared as previously described in Floudas, D. et al. Science 336, 1715-1719 (2012).
5-10ug of gDNA was sheared to >10kb using g-tube (Covaris). The sheared DNA was treated with DNA damage repair mix followed by end repair and ligation of SMRT hairpin adapters using SMRTbell Template Preparation Reagent Kit (Pacific Biosciences). Fragments without adaptors are digested with exonuclease. Libraries were sequenced on Pacific Biosciences RSI sequencer using standard protocols.

tag: strain


title: Arabidopsis thaliana (Col-0, 11 days)

data_processing:
SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: TAIR10
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference.  The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files

source_name: Arabidopsis thaliana (Col-0, 11 days) _Whole organism

extract_protocol:
A. thaliana seeds were surface sterilized with 70% ethanol, then stratified at 4 degrees celsius for 2 days. Seeds were then sown on 1/2 Murashige and Skoog media containing 1% agar, and grown vertically for 11 days under short-day photocycles at 22 degrees celsius (8 hr light/ 16 hr dark) at a density of about 100 seeds per 10cm2 plate. Genomic DNA was prepared as manufacturer’s instruction.
5-10ug of gDNA was sheared to >10kb using g-tube (Covaris). The sheared DNA was treated with DNA damage repair mix followed by end repair and ligation of SMRT hairpin adapters using SMRTbell Template Preparation Reagent Kit (Pacific Biosciences). Fragments without adaptors are digested with exonuclease. Libraries were sequenced on Pacific Biosciences RSII sequencer using standard protocols.

tag: treatment

value: grown for 11 days


title: Tobacco_Whitefly infested

description: After 72 h of feeding

tag: stess

value: whitefly infested


title: Tobacco_TYLCCNV and whitefly co-infested

description: After 72 h of feeding


title: Chlamydomonas reinhardtii, replicate 2 (4A+, 48h post Nitrogen depletion)

data_processing:
SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: C.Reinhardtii_236 (JGI Phytozome assembly V5.0)
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference.  The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files [Chlamy.modifications.48H.Rep1and2.gff.gz, Chlamy.modifications.48H.Rep1and2.csv.gz]

source_name: Chlamydomonas reinhardtii, replicate (4A+, 48h post Nitrogen depletion) _Whole organism

extract_protocol:
C. reinhardtii wild type strain 4a+ were cultured using Tris-acetate-phosphate (TAP) medium in Erlenmeyer flasks at 25 degrees Celsius with agitation at 180 rpm under light irradiation at 100 microE. Cells were washed twice with nitrogen-free media and re-suspended to a density of 2 x 106 cells/ml and harvested at 48 hr post starvation. Cells were lysed using lysis buffer (50mM Tris-HCl pH 8, 200mM NaCl, 2mM EDTA, 2% SDS and proteinase K) and genomic DNA was extracted using CTAB-based protocol39.
5-10ug of gDNA was sheared to >10kb using g-tube (Covaris). The sheared DNA was treated with DNA damage repair mix followed by end repair and ligation of SMRT hairpin adapters using SMRTbell Template Preparation Reagent Kit (Pacific Biosciences). Fragments without adaptors are digested with exonuclease. Libraries were sequenced on Pacific Biosciences RSII sequencer using standard protocols.

value: 48h post Nitrogen depletion


title: Chlamydomonas reinhardtii, replicate 1 (4A+, 48h post Nitrogen depletion)


title: goat mammary gland from dry-off (G) RNA-Seq data rep2

tag: breed

tag: age/developmental stage

value: 310 days postpartum


title: Chlamydomonas reinhardtii, replicate 2 (4A+, log phase)

data_processing:
SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: C.Reinhardtii_236 (JGI Phytozome assembly V5.0)
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference.  The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files [Chlamy.modifications.WT.Rep1and2.gff.gz, Chlamy.modifications.WT.Rep1and2.csv.gz]

source_name: Chlamydomonas reinhardtii, replicate (4A+, log phase) _Whole organism

extract_protocol:
C. reinhardtii wild type strain 4a+ were cultured using Tris-acetate-phosphate (TAP) medium in Erlenmeyer flasks at 25 degrees Celsius with agitation at 180 rpm under light irradiation at 100 microE. Cells were harvested at mid-log phase (at approximately 2 x 106 cells/ml). Cells were lysed using lysis buffer (50mM Tris-HCl pH 8, 200mM NaCl, 2mM EDTA, 2% SDS and proteinase K) and genomic DNA was extracted using CTAB-based protocol39.
5-10ug of gDNA was sheared to >10kb using g-tube (Covaris). The sheared DNA was treated with DNA damage repair mix followed by end repair and ligation of SMRT hairpin adapters using SMRTbell Template Preparation Reagent Kit (Pacific Biosciences). Fragments without adaptors are digested with exonuclease. Libraries were sequenced on Pacific Biosciences RSII sequencer using standard protocols.

tag: growth phase

value: log phase


title: Chlamydomonas reinhardtii, replicate 1 (4A+, log phase)


title: Phf7-bam- rep1

description: oligo-dT selected RNA

tag: genotype/variation

value: Testis

value: Within 3 days of eclosion