title: ADAR1E912A_rep1

city: LA

first: Jaegyoon

last: Ahn

address: 611 Charles E. Young Drive

department: IBP

institute: UCLA

data_processing:
Small RNA-Seq reads were first processed to remove adapter sequences and low quality reads. Number of occurrences of each small RNA species was calculated following adapter removal.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files contain sRNA abundance.

source_name: U87MG (Glioblstoma;Astrocytoma)

growth_protocol: U87MG cells were purchased from American Type Culture Collection (ATCC). Cells were maintained in DMEM high glucose medium supplemented with pyruvate, L-glutamine, and 10% fetal bovine serum (FBS) (Gibco, Life Technologies).

extract_protocol:
For small RNA extraction, total RNA was isolated using QIAzol. Spike-in controls (Exiqon) were added at a level of one reaction volume per one μg of total RNA. Small RNAs were isolated using miRNeasy mini kit (Qiagen).
For small RNA-seq,  Spike-in controls (Exiqon) were added at a level of one reaction volume per one μg of total RNA. Small RNA sequencing libraries were generated using Illumina TruSeq Small RNA library prep kit according to the manufacturer’s instruction.

treatment_protocol: For small RNA-seq, U98MG cells were transfected with one of the following: (1) siRNA of ADAR1 (Bahn et al., 2012), (2) a scrambled siRNA as control, (3) expression vector of wildtype ADAR1, (4) expression vector of ADAR1 EAA mutant, (5) a control vector (pcDNA4, Invitrogen) and incubated for 36h, (6) expression vector of ADAR1 E912A mutant.

tag: passages

tag: transfected with

tag: molecule subtype

value: small RNA


title: dCas9+ALL IL1RN_rep2

status: Public on Mar 11 2015

type: SRA

city: Durham

first: Christopher

last: Vockley

state: NC

address: 101 science drive rm 2193

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie2-align version 2.1.0, and the  -p 32 --end-to-end --very-sensitive t" alignment options
Reads were converted from .sam to .bam files using samtools view version 0.1.19-44428cd with the  "-bS" option
Bam files were sorted using Samtools sort version 0.1.19-44428cd with the options "32 -m 2G"
Bam files were indexed using Samtools Index version 0.1.19-44428cd
Duplicate reads were removed using samtools rmdup  version 0.1.19-44428cd  usint the "-s option"
Bam files were re-indexed after duplicates were removed using Samtools Index version 0.1.19-44428cd
Reads were counted using samtools idxstats version 0.1.19-44428cd
Differential expression was computed using R version 3.1.2 using the DEseq2 package version 1.6.2  with default settings
Genome_build: RefSeq transcripts from hg19
Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript.

molecule: total RNA

organism: Homo sapiens

source_name: Cultured HEK293T cells

growth_protocol: HEK293T cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cel Culture Facilities and were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Between 0.5-1 million cells were washed with PBS and then lysed using Qiagen RLT buffer. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was prepared using the Wafergen automated sample prep system with the Prep-x mRNA kit with 1 microgram of total RNA.
Libraries were prepared using the Apollo 324 liquid handling platform, as per manufacturer’s instruction using the prep-mRNAseq kit.

treatment_protocol: HEK293T cells were transfected with Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions. Transfection efficiencies were routinely higher than 80% as determined by fluorescence microscopy following delivery of a control eGFP expression plasmid. Cas9 expression plasmids were transfected at a mass ratio of 3:1 to the total amount of gRNA expression plasmids as in main text.

tag: cell line

tag: transfected gene

tag: guide rna at 4 sites


title: Ad-NERKI, 10 nM E2, rep 2

city: Rochester

first: David

middle: George

last: Monroe

state: MN

address: 200 1st St SW

department: Endocrinology

institute: Mayo Clinic

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and count values for each Sample

source_name: hFOB 1.19 cells

growth_protocol: The hFOB 1.19 human fetal osteoblastic cell line (hFOB) was passaged in phenol red-free αMEM growth medium (Invitrogen, Carlsbad, CA) supplemented with 1X antibiotic/antimycotic (Invitrogen), 10% (v/v) fetal bovine serum (Hyclone, Logan, UT) and 300 ug/mL G418 selection antibiotic.

extract_protocol:
Total RNA was prepared using RNeasy minicolumns (Qiagen, Valencia, CA) and treated with RNase-free DNase (Qiagen) to remove potential contaminating DNA.
RNA libraries for RNAseq analysis were prepared from 100 ng of isolated total RNA from each sample using the manufacturer’s instructions. Unique indexes were incorporated at the adaptor ligation step for loading multiple samples per flow cell.  Three distinct indexed libraries were loaded per flow cell and sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8).  Base calling was performed using Illumina RTA (version 1.12.4.2).  An average of 130 million reads per sample was achieved resulting in ~96% mapped reads.

treatment_protocol: hFOB cells were plated in 10-cm culture dishes (n=6) at a final density of 2 × 10^4 cells/cm2.  Cells were infected at the time of plating at a multiplicity of infection (MOI) of 15 (Ad-ERα), 30 (Ad-NERKI) and 22.5 (Ad-NOER).  Following another 24 hour incubation to allow for complete infection, the cells were treated with either ethanol vehicle (0.1% v/v) or 10 nM 17-β-estradiol (0.1% v/v; Sigma-Aldrich) in the presence of media containing triple-stripped charcoal-treated FBS for an additional 24 hrs.

tag: cell type

value: osteoblastic cell


title: Ad-Era, 10 nM E2, rep 2


title: VP64+ALL IL1RN_rep2


title: dCas9-p300 D1399Y_rep1


title: Ad-NERKI, Vehicle, rep 2


title: Ad-Era, Vehicle, rep 2


title: Ad-NOER, 10 nM E2, rep 1


title: dCas9-p300 core_rep1

value: dCas9-p300 core


title: dCas9-VP64_rep1


title: Ad-Era, Vehicle, rep 3


title: Ad-NOER, Vehicle, rep 1


title: dCas9-VP64_rep3


title: D1399Y+ALL IL1RN_rep2


title: dCas9_rep1


title: Ad-NERKI, 10 nM E2, rep 1


title: Mel202 DD-mut-SF3B1 plus Shld (2 days)

city: Dedham

first: Adnan

last: Derti

state: MA

address: 100 Alden Street

department: Bioinformatics

institute: personal

description: mutant-SF3B1-specific Degron knockdown

data_processing:
Methods are described in detail in "A chemical genetics approach for the functional assessment of novel cancer genes", Zhou et al. (submitted). Briefly, reads were aligned to the reference human genome (hg19) with a modified version of Tophat using UCSC KnownGene as a reference.
For each sample, transcripts were assembled using CLASS with KnownGenes as the reference. All assemblies were then merged with Cuffmerge.
Gene expression was quantified using Cufflinks with the merged CLASS transcripts as the reference.
Expression levels were rescaled so that the upper quantile gene expression value in each sample was 10.
Genome_build: hg19
Supplementary_files_format_and_content: matrix listing rescaled gene expression values, with CLASS/Cuffmerge identifier and HUGO or KnownGene gene if applicable.

source_name: MEL202 cell line

extract_protocol:
The gel-free protocol was employed for the TruSeq RNA Sample Prep Kit per manufacturer’s specifications, and performed on the Beckman Coulter Biomek FXp robotics platform. The standard RNA fragmentation profile was used as recommended by Illumina (94 degrees Celsius for 8 minutes). The PCR-amplified RNA-seq library products were then quantified using the Advanced Analytical Fragment Analyzer Standard Sensitivity NGS Fragment Analysis Kit (catalog number DNF-479). The samples were diluted to 10 nanomolar in Qiagen Elution Buffer (Qiagen material number 1014609), denatured, and loaded at 2.75 picomolar on an Illumina HiSeq2500 in Rapid Run mode using TruSeq Rapid PE Cluster Kit  – HS (catalog number PE-402-4001) and TruSeq Rapid SBS Kit – HS (200 cycle) reagents (catalog number FC-402-4001).
The RNA-seq libraries were sequenced at 100 base-pair paired-end with a 7-base-pair index using the standard Illumina primers. The sequence intensity files were generated on the instrument using the Illumina Real Time Analysis software. The intensity files were demultiplexed and fastq files created using the CASAVA 1.8.2 software suite.

tag: clone

value: DD-mut-SF3B1 (2 days)

tag: treatment

value: plus Shld


title: Mel202 DD-wt-SF3B1 minus Shld (2 days)

description: wildtype-SF3B1-specific Degron knockdown

value: DD-wt-SF3B1 (2 days)

value: minus Shld


title: Mel202 mut-SF3B1 KO plus Shld (2 days)

description: mutant-SF3B1 knockout

value: mut-SF3B1 KO (2 days)


title: Mel202 parental cells repeat #1 minus Shld

description: parental MEL202 cells

value: parental cells repeat #1


title: Ad-Era, 10 nM E2, rep 1


title: Ad-Era, Vehicle, rep 1


title: Ad-NERKI, Vehicle, rep 1


title: Mel202 DD-wt-SF3B1 plus Shld (2 days)


title: siADAR1_rep2

state: CA

data_processing:
Small RNA-Seq reads were first processed to remove adapter sequences and low quality reads. The reads were then aligned to hg19 using Bowtie allowing at most 1 mismatch. The mapping results were parsed to identify reads mapped to miRNAs (miRBase, Release 19). Only reads mapped uniquely to the miRNAs were retained. In parallel, reads were also aligned to the spike-in controls allowing no mismatches. The number of reads mapped to each miRNA was normalized using the spike-in controls and total number of mapped reads in each library.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files contain sRNA abundance.

value: Glioblastoma (Astrocytoma) cells

value: ADAR1 siRNA


title: PCDNA4_rep1

value: control vector (pcDNA4)


title: PCDNA4_rep2


title: siControl_rep2

source_name: siControl

value: control siRNA


title: ADAR1OE_rep2

value: ADAR1 overexpression vector


title: siControl_rep1


title: ADAR1EAA_rep2

value: ADAR1 RNA binding mutant (EAA)


title: ADAR1EAA_rep1


title: ADAR1OE_rep1


title: Mel202 parental cells repeat #1 plus Shld

description: parental MEL202 cells


title: Adar1ClipAB2

description: ADAR1CLIP RNA

data_processing:
library strategy: CLIP-seq
Adapter sequences were trimmed from both ends of the raw CLIP-Seq reads using cutadapt v1.1. The 5' and 3' end adapter sequences were examined to determine the strand of the read relative to its corresponding RNA. Reads shorter than 15nt after adapter-trimming were discarded.
Clip-seq reads were mapped to hg19 using Novoalign v2.08.22. The alignment parameters were: “-o FullNW –t 150 –R 99 –r All –F STDFQ –o SAM”. A step-wise mapping procedure was applied.  (1) Reads that aligned to the rRNA sequences from UCSC genome browser were discarded. (2) Reads passing the rRNA filter were aligned to the Alu sequences located in RefSeq genes. (3) Reads that did not map to Alu sequences in (2) were aligned to hg19. (4) Alignment results from (2) and (3) were filtered based on the number of mismatches (7% of each read length after adapter-trimming) and merged. (5) The paired-end reads were examined for their concordance by considering the corresponding mapped chromosome, mapped strand, and the distance between the pair of reads.
Peaks were called using following procedure: Mapped reads were classified as sense- and antisense-reads based on the strand of the reads and RefSeq annotations. Only sense reads were used to define binding clusters. In each dataset, we removed duplicate reads and kept the one with the least mismatches. The reads were retained for further analysis if they overlapped with pre-mRNAs annotated by RefSeq. A sliding window (83nt) was applied to determine whether the number of reads in the window exceeded expected values based on both a local and global read frequency. A Poisson model was used to test the significance of read enrichment in each window. The local frequency, specific for each gene, was calculated as the number of reads overlapping that gene divided by gene length. The global frequency was defined for all transcripts in the genome.  A Bonferroni-corrected p value cutoff of 0.001 was applied to call significant clusters. The final clusters were classified as Alu and non-Alu clusters based on the annotations from UCSC genome browser repeat track. The stringent set of binding clusters was defined as those common to both ADAR1 CLIP experiments. To remove possible non-protein specific CLIP artifacts, we further filtered all clusters by removing those common to at least 2 other public CLIP data sets.
Genome_build: hg19
Supplementary_files_format_and_content: Bed file contains clip clusters from both ADAR1ClipAB1 and ADAR1ClipAB2 read alignment results.

extract_protocol:
For CLIP-seq, RNA was extracted using acid phenol extraction methods.
For CLIP-seq library, Universal miRNA cloning linker (5’-rAppCTGTAGGCACCATCAAT-NH2-3’, NEB) was used as 3’ linker and 5’ linker was (5’-AGGGAGGACGAUGCGG-3’). PCR amplification was run for 23 cycles with 98°C 10s, 55°C 30s, 72°C 30s. PCR products were run on a 4% PAGE gel for size selection (75bp-250bp) and purified by phenol extraction. Sequencing library was prepared using the Encore NGS library kit (NuGEN) and sequenced.

treatment_protocol: CLIP-seq was performed according to previous methods with some modifications (Ule, 2005). Briefly, U87MG cells were harvested at 90% confluency. Cells were washed once with 10ml ice-cold PBS. 254nm UV crosslink 2 × 800mJ/cm2 was treated with samples on ice.

tag: pasaages

tag: clip antibody

value: ADAR1 mouse monoclonal

tag: clip antibody vendor

value: Santa Cruz Biotechnologies

tag: clip antibody cat. #


title: Adar1ClipAB1

description: ADAR1CLIP RNA


title: ASXL1(1-479)+BAP1 RNA-Seq_rep2

city: La Jolla

first: Anjana

last: Rao

address: 9420 Athena Circle

department: Department of Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

description:
Ribosome-depleted RNA
processed data file: rna_express_lib3and4.xprs.txt; DESeq_results.txt

data_processing:
RNA-seq reads were aligned using TopHat (version 2.0.9). Differential expression results were made with HTSeq and DESeq using genome version mm9 and Ensembl annotation (release 67, excluding non-protein coding transcripts). eXpress was used to obtain transcript-level expression estimates.
Genome_build: mm9
Supplementary_files_format_and_content: BED files with SICER calls, DESeq result file, eXpress result files

organism: Mus musculus

source_name: ASXL1(1-479)+BAP1 RNA-Seq

growth_protocol: EML cells cultured under conditions recommended by ATCC. ATCC Cat # CRL-11691

extract_protocol:
Total RNA was isolated and subjected to ribosomal depletion using Ribozero GOLD kit purchased from Epicentre.
RNA-seq library construction was carried out using 5500XL sequencing.

treatment_protocol: EML cells were transduced with either MSCV-IRES-GFP (MiG-empty) or with retroviral constructs encoding ASXL1(1-479) + BAP1 and expanded for 15 days post-transduction

value: EML

tag: tissue

value: bone marrow

value: basophil

tag: atcc catalog number


title: ASXL1(1-479)+BAP1 RNA-Seq_rep1


title: Mel202 DD-mut-SF3B1 minus Shld (2 days)

description: mutant-SF3B1-specific Degron knockdown

value: DD-mut-SF3B1 (2 days)


title: MiG-empty RNA-Seq_rep1

description:
Ribosome-depleted RNA
processed data file: rna_express_lib1and2.xprs.txt; DESeq_results.txt

source_name: MiG-empty RNA-Seq


title: ADAR1E912A_rep2

value: small RNA


title: MiG-empty RNA-Seq_rep2


title: Mel202 mut-SF3B1 KO minus Shld (2 days)

description: mutant-SF3B1 knockout


title: siADAR1_rep1


title: MiG-empty input DNA rep2

library_source: genomic

data_processing:
ChIP-seq reads were aligned using Bowtie (version 0.12.8), allowing only uniquely mapping reads, fragment sizes of 90-250bp, and removing duplicates.
Enriched areas were called using SICER with parameters as suggested in the documentation and for H2AK119Ub with win size=800 and gap size=2400.
Genome_build: mm9
Supplementary_files_format_and_content: BED files with SICER calls, DESeq result file, eXpress result files

molecule: genomic DNA

source_name: MiG-empty input DNA

extract_protocol:
IP's for ChIP-seq were carried out on mono-nucleosomes generated from EML cells.
ChiP-seq libraries were constructed using NEB's ChIP-seq library preparation kit for SOLiD sequencing.

tag: chip antibody

value: none (input)


title: MiG-empty input DNA rep1


title: H3K27me3 MiG-empty ChIP-seq rep2

description: processed data file: peaks_H3K27me3.bed

source_name: H3K27me3 MiG-empty ChIP-seq

value: H3K27me3 (Cell Signaling Technologies (Danvers, MA), Cat# 9733)


title: H3K27me3 MiG-empty ChIP-seq rep1

description: processed data file: peaks_H3K27me3.bed


title: H3K4me3 MiG-empty ChIP-seq rep2

description: processed data file: peaks_H3K4me3.bed

source_name: H3K4me3 MiG-empty ChIP-seq

value: H3K4me3 (Cell Signaling Technologies (Danvers, MA), Cat# 9727)


title: H2AK119Ub MiG-empty ChIP-seq rep1

description: processed data file: peaks_H2AK119Ub.bed

source_name: H2AK119Ub MiG-empty ChIP-seq

value: H2AK119Ub (Cell Signaling Technologies (Danvers, MA), Cat# 8240)


title: H2AK119Ub MiG-empty ChIP-seq rep2


title: H3K4me3 MiG-empty ChIP-seq rep1

description: processed data file: peaks_H3K4me3.bed


title: DYRK1A_Cycling_T98G

city: Barcelona

first: Chiara

last: Di Vona

state: Spain

address: Carrer Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: CRG

data_processing:
The reads were aligned to the hg19 human reference genome using bwa, allowing up to 3 mismatches and no gaps (whereby >97% of the reads were aligned).
Resulting SAM files were sorted by position and transformed to BAM using samtools. Picard (http://picard.sourceforge.net) was used to mark clonal duplicate reads in the BAM files (e.g. ~20% duplicate reads marked in TG98G).
The ChIP-Seq peak caller ‘shore peak’ from the package SHORE (Ossowski et al., 2010) (http://sourceforge.net/projects/shore/) was used for the calling and visualization of peaks. BAM files were converted to the native SHORE format map.list using ‘shore convert’, and the peaks were predicted by the peak caller ‘shore peak’, using only uniquely aligned reads and allowing for up to 3 duplicate reads at a position.
Peaks were accepted when: i) fold-change (FC, DYRK1A IgG versus control IgG) was ≥ 3; ii) the false discovery rate (FDR) was ≤ 0.05; iii) peak size was at least 80 bp; and iv) the x-shift (distance between forward and reverse peak) was at least 10 bp.
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated text file containing peak coordinates, peak id and peak ranking.

source_name: Brain

growth_protocol: Both HeLa and T98G cell lines were supplied by the American Type Culture Collection (http://www.atcc.org). All the cell lines were cultured at 37ºC and in 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS; Invitrogen) and supplemented with antibiotics (100 u/ml penicillin and 100 µg/ml streptomycin; Invitrogen).

extract_protocol:
Formaldehyde was added to the culture medium to a final concentration of 1% for 10 min at RT and the crosslinking was then quenched with 0.125 M glycine for 5 min. Crosslinked cells were washed twice with TBS, resuspended in 1 ml of Buffer I (5 mM PIPES [pH 8.0], 85 mM KCl, 0.5% NP-40 plus PIC) and incubated on ice for 10 min. Cells were centrifuged at 800 x g for 5 min, and the cell pellet was resuspended in 1.2 ml of Buffer II (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.0], 1 mM phenylmethylsulfonyl fluoride and PIC) and incubated for a further 10 min on ice. Samples were centrifuged and the cell pellet was resuspended in 1.2 ml of IP Buffer (100 mM Tris-HCl [pH 8.6], 0.3% SDS, 1.7% Triton X-100 and 5 mM EDTA) prior to sonicating the chromatin to an average size of 200-500 bp (Bioruptor, Diagenode). Extracts (600 μg of total protein) were diluted in 1 ml of IP Buffer and immunoprecipitated overnight at 4°C with the corresponding antibodies (listed in the Supplemental Tables for Extended Experimental Procedures) or control IgG antibodies. Immune complexes were recovered by incubating for 4 h at 4°C with protein G-Sepharose beads (40 ml), and the beads were then washed with three successive 1 ml washes in Low salt Buffer III (50 mM HEPES [pH 7.5], 140 mM NaCl, 1% Triton X-100 plus PIC), and one wash with High salt Buffer IV (50 mM HEPES [pH 7.5], 500 mM NaCl, 1% Triton X-100 plus PIC).
Libraries were prepared using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® kit (ref. E6200S) according to the manufacturer's protocol. Briefly, 10 ng of input and ChIP enriched DNA were subjected to end repair, addition of “A” bases to 3′ ends and ligation of SE adapters. All purification steps were performed using Qiagen PCR purification columns (refs. 50928106 and 50928006). Library size selection was done with 2% low-range agarose gels. Fragments with average insert size of 280 bp were cut from the gel, and DNA was extracted using QIAquick Gel extraction kit (ref. 50928706, Qiagen) and eluted in 36 µl EB. Library amplification was performed by PCR on the size selected fragments using the following primers: PCR primer 1.1: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ PCR primer 2.1: 5’-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT-3’ . Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s Cluster Station. Libraries were loaded at a concentration of 7 pM onto the flowcell, and were sequenced 1 x 36 on Illumina’s Genome Analyzer IIx.

treatment_protocol: For serum starvation conditions, T98G cells were grown in DMEM without FBS for 48 h.

tag: tissue origin

value: Brain

value: Glioblastoma

value: DYRK1A antibody (ab69811)

tag: chip antibody vendor

value: Abcam


title: DYRK1A_Cycling_HeLa

source_name: Cervix

value: HeLa

value: Cervix

value: Adenocarcinoma


title: DYRK1A_SerumStarved_T98G

tag: growing conditio

value: serum starvation


title: CTRL, 2961-TA-46

status: Public on Mar 10 2015

city: Nashville

first: Charles

middle: F

last: Spurlock III

state: Tennessee

address: 1161 21st Avenue South

department: Medicine

institute: Vanderbilt University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads.
Alignment to human genome (hg19) using TopHat 2.
Read count quantification using HTSeq.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs.

source_name: Peripheral whole blood draw, healthy control

extract_protocol:
Peripheral whole blood was collected into PaxGene tubes. RNA was isolated per the manufacturer's supplied protocol.
Total RNA isolated from PaxGene tubes was purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNase treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
2343 and 2961 libraries were constructed using the Illumina TruSeq Stranded mRNA kit (Cat. No. RS-122-2101) following the manufacturer's supplied protocol.

value: peripheral whole blood

tag: disease state

value: healthy


title: IgG_T98G

tag: cell line

value: rabbit IgG (sc-2027)

value: Santa Cruz Biotechnology


title: CTRL, 2961-TA-44


title: RRMS, 2961-TA-39

source_name: Peripheral whole blood draw, RRMS

value: relapsing-remitting multiple sclerosis (RRMS)


title: CTRL, 2343-TA-4


title: RRMS, 2343-TA-3


title: RRMS, 2961-TA-41


title: HER2 siRNA knockdown, replicate 3

city: Cleveland

first: Ahmad

middle: M

last: Khalil

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Next generation RNA sequencing of BT474 cells: After RNA was isolated from BT474 samples, we assessed the quality of RNA using BioRad Experion. RNA samples with RNA integrity number (RIN) larger than 8 (max is 10) were considered high quality and suitable for RNA-seq.  Library preparation was performed using Scriptseq™ Complete Gold (Human/Mouse/Rat) (Illumina) and sequenced on Illumina Hi-Seq2500. Six samples were run on a single flow cell.  We generated 100 bp paired-end strand-specific sequences, which were mapped to human genome release hg19 using TopHat with 2 mismatches allowed for full-length reads.  The raw reads were mapped to human genes annotated in RefSeq database and lincRNAs annotated in Cabili et al. [4] using Cufflinks V2.0.2, and subsequently used for differential gene expression analysis after normalizing the values to the total mapped reads in each sample, see supporting file 14. Expression values were calculated as FPKM (fragment per kilobase of exon per million of mapped fragments) and were used to determine expression of both lincRNAs and mRNAs in HER2 knock down (KD) and negative control (NC) siRNA samples. Transcripts were considered expressed if FPKM values across either all BT474 HER2 KD samples or all NC samples were ≥ 1.0 for mRNAs and ≥ 0.25 for lincRNAs. The mean expression level was calculated, and from this statistically significant differences in expression between HER2 KD samples and NC samples was determined using a paired t-test in R. Additionally, fold changes (HER2 KD / NC) were calculated to identify differentially expressed transcripts. Transcripts were deemed differentially expressed if the fold change was ≥ 2.0 or ≤ 0.5.
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, there are two processed data .txt files.  The lincRNA files contain the XLOC number of the lincRNA described in Cabili et al., 2011 and the normalized FPKM value to the total mapped reads in each sample.  The mRNA file contains the  RefSeq database gene ID with corresponding normalized FPKM value.

source_name: HER2 siRNA knockdown

growth_protocol: BT474 cells were grown in Hybri-Care Medium (ATCC® 46-X™) supplemented with 10% fetal bovine serum, 100 units/ml of Penicillin, and 100 μg/ml Streptomycin  at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using RNeasy® Mini Kit (Qiagen) according to the manufacturer’s protocol.  An added DNase (Qiagen) treatment step was included after the first wash.
Library prepartion as per Illumina Scriptseq Complete Gold (Human/Mouse/Rat) instructions including Ribo-Zero Gold rRNA Removal Reagents.

treatment_protocol: siRNA knockdown of  HER2 was achieved through the transfection of HER2-specific siRNAs (Life Technologies, Cat # 4390824, s611 and s613 ) at a final concentration of 15 nM with Lipofectamine RNAiMax at 7.5 μL/well of 6-well plate.  Negative control siRNA #1 and #2 (Ambion Cat. # AM4611 and AM4613) were used as negative controls for the HER2 knockdown.

tag: cell line origin

value: female caucasian with ductal carcinoma

value: breast cancer cell line

tag: transfected with

value: HER2-specific siRNAs


title: HER2 siRNA knockdown, replicate 2

tag: cell type


title: HER2 siRNA knockdown, replicate 1


title: Negative Control siRNA, replicate 1

source_name: Neg Control siRNA

value: negative control siRNAs


title: dmP0

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced clean reads were mapped to Drosopholia melanogaster (dmel-all-chromosome-r5.45.fasta/Ensembl) whole genome using tophat v2.0.12 with parameters --bowtie1 --no-coverage-search --segment-length 20 -g 10 -p 10
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.1) with the provision of a GTF annotation file (Drosophila_melanogaster.BDGP5.73.gtf).
Gene expression differences were assessed by Cuffdiff use classic FPKM, with false discovery rate correction for multiple testing.
Genome_build: tair10

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Head of adult male flies

growth_protocol: all flies used were grown and kept in normal fly food

extract_protocol:
Trazol-total RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: Sex

value: male

value: head


title: Negative Control siRNA, replicate 2


title: CTRL, 2961-TA-48


title: IgG_HeLa


title: RRMS, 2343-TA-2


title: rictor1


title: epmA_lb

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: mRNA: ribosome footprints

data_processing:
Reads with N bases or Phred < 20 were dropped. The linker sequence was trimmed, and reads mapping to rRNA or tRNA sequences were subtracted.
Remaining reads were mapped to the E coli K12 MG1655 genome using bowtie.
Genome_build: NC_000913ver2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, with 3'-assignment method, normalized by number of reads.

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

source_name: cell cultures

growth_protocol: 400 mL cultures were grown to OD600 of 0.4, filtered, and flash frozen in liquid nitrogen.

extract_protocol:
Cell pellets were lysed in a freezer mill, clarified, digested with MNase, and monosomes were purified over a sucrose gradient (except cw31).
RNA fragments 20 - 40 nt in length were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.

tag: genotype/variation

value: epmA

tag: media

value: LB

tag: monosome purification

value: sucrose gradient


title: lst81dmP0


title: CTRL, 2961-TA-43


title: CTRL, 2961-TA-45


title: epmB_lb

description: mRNA: ribosome footprints

value: epmB


title: Negative Control siRNA, replicate 3


title: CTRL, 2961-TA-47


title: epmC_lb

description: mRNA: ribosome footprints

value: epmC


title: RRMS, 2961-TA-42


title: wt_lb_rep2

description: mRNA: ribosome footprints

value: wild type


title: efp_lb_rep1

description: mRNA: ribosome footprints

value: efp


title: W1118


title: wt_lb_rep1

description: mRNA: ribosome footprints


title: RRMS, 2961-TA-40

value: peripheral whole blood


title: efp_lb_rep2

description: mRNA: ribosome footprints


title: epmC_mops

description: mRNA: ribosome footprints

value: MOPS


title: TargetSeq-Untreated9

status: Public on Mar 16 2015

city: Stanford

first: Jiang

last: Li

address: 269 Campus Drive, Stanford University

department: Dermatology

institute: Stanford University

data_processing:
Reads were aligned to the human reference genome sequence (hg19) using the BWA aligner. Samtools mpileup was used to call variants. Only bases meeting the minimum base quality score of 20 from reads meeting the minimum mapping quality score of 20 were considered. A minimum allele frequency of 5% at a position with a read depth > 100 was required to make calls.
Identified variants were annotated using SeattleSeq138 to exclude non-pathogenic variants reported in dbSNP138 and to identify variants that had nonsynonymous consequences or affected splice sites.
Genome_build: hg19
Supplementary_files_format_and_content: excel file  containing all the variants from all the target resequencing

source_name: untreated basal cell cancers

extract_protocol:
5-8 10um sections were obtained from the FFPE tumor block and DNA was isolated using the Qiagen DNeasy Blood and Tissue kit according to manufacturer’s protocol (Qiagen). The exonic regions of PTCH1 and SMO were amplified using the Access Array platform (Fluidigm).
The samples were amplified in a multiplex format with genomic DNA (100 ng) according to the manufacturer's recommendation (Ambry Genetics). Subsequently, the multiplexed library pools were subjected to deep sequencing using the Illumina MiSeq platform.

value: basal cell carcinomas (BCCs)

tag: response to smoothened (smo) inhibitors

value: N/A (Untreated)


title: epmA_mops

description: mRNA: ribosome footprints


title: epmB_mops

description: mRNA: ribosome footprints


title: efp_mops_rep2

description: mRNA: ribosome footprints


title: efp_mops_rep1

description: mRNA: ribosome footprints


title: wt_mops_rep2

description: mRNA: ribosome footprints


title: lst81

tag: tissue


title: wt_mops_rep1

description: mRNA: ribosome footprints


title: wt_lbcol_rep2

description: mRNA: ribosome footprints

value: spin column


title: Spleen RUN2 L008

city: Paris

first: Giovanni

last: Bussotti

address: 25-28 Rue du Dr Roux

country: France

institute: Institute Pasteur

description:
biological replicate 1
library strategy: Targeted RNA Sequencing (CaptureSeq)

data_processing:
Illumina Casava1.7 software used for basecalling.
Before mapping FastQC was utilized to confirm sequence quality. Reads were trimmed with the Trim Galore Cutadapt11 wrapper using the –paired option.
For K562 and PBMC ERCC capture, sequenced reads (.fastq files) were aligned to the human genome using Tophat2 12 with the firststrand library type option selected. A human Bowtie213 index containing the ERCC controls was utilized for Tophat2 mapping, along with a transcriptome index.
For lncRNA capture from tissues and cell lines, sequenced reads (.fastq files) were aligned to the human genome using STAR 14. A reference annotation from GENCODE V19 was supplied during alignment. A splice junction library file was then derived from alignments and used for a second-round alignment solely using TopHat2 12.
To reduce memory requirements and improve runtimes the lncRNA cell line capture samples were preprocessed with trinity’s read normalization 17 release 2013-02-25 with parameter --max_cov 30. Reads from separated sequencing runs and lanes were mapped to the human genome (GRCh37, ENSEMBL 74) considering GENCODE version 19 reference annotations using STAR 14 version 2.3.1z with parameters --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout. The resulting sam files were processed to remove the soft-clipping. Transcriptome assemblies were generated using cufflinks version 2.1.1 masking rRNA genes and providing the parameters -u --library-type fr-firststrand -b. The comprehensive transcriptome assembly (merged_transcript_assembly.gtf) was generated merging the individual assemblies with cuffmerge version 2.1.1, and selecting with bedtools intersect v2.19.1 the transcript overlapping the capture probes. The gene expression was estimated by merging for each tissue the individual mapping files with samtool version 0.1.19-44428cd. Then the gene counts for each tissue (norm.counts.tsv) were estimated by HTSeq (version 0.6.1) and normalized by DESeq2 (version 1.2.10)
Genome_build: hg19

source_name: Spleen

growth_protocol: Human K562, MCF-7 and SK-N-SH cells were purchased from Cellbank. All cell lines were cultured at 37°C, 5% C02 with ten percent fetal bovine serum and penicillin/streptomycin. K562 and HeLa cells were cultured in RPMI and DMEM respectively, MCF-7 and SK-N-SH cells were cultured in MEM. Briefly, RNA was extracted by TRIzol, DNase treated with Turbo™ DNase (Life Technologies), confirmed DNA-free4 and its integrity confirm by Agilent 2100 Bioanalyzer (Agilent Technologies). 5 μg quantities of RNA were ribodepleted with Ribo-Zero™ (Epicentre). The Ambion® FirstChoice® Human Total RNA Survey Panel (Life technologies) was utilized to examine 20 human tissues. 5 μg quantities of RNA were ribodepleted with Ribo-Zero™ (Epicentre) and successful rRNA removal validated with Agilent 2100 Bioanalyzer (Agilent Technologies). Collection and RNA extraction from peripheral blood mononuclear cells (PBMCs) Whole blood was collected from individuals (Princess Alexandra Hospital REC approval 2005/221). PMBCs were purified by a ficoll gradient and RNA extracted by TRIzol. Purified RNA was prepared for Capture as per cell line RNA.

extract_protocol: Capture sequencing was performed by combining and modifying the NimbleGen SeqCap EZ Library SR User’s Guide V3.0 and the NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery v3.2. RNA sequencing libraries of ribodepleted total RNA from three K562 biological replicates were created using the TruSeq® Stranded mRNA Sample Preparation Kit (Illumina). Different index adaptors (4,6,12) were added to each K562 biological replicate. Library input consisted of ribodepleted RNA from 5 μg original total RNA after quality checking. ERCC RNA Spike-In Control mix 1 (Invitrogen) was added to ribodepleted RNA to give a final ERCC concentration of 1% (replicate 1 and 2) and 1.08% (replicate 3). Library preparation was begun at the fragmentation step by the addition of 9 μl EPH buffer and the standard protocol followed until “Enrich DNA Fragments”. The 20 μl obtained at the end of the “Ligate Adaptors” step was increased to 21 μl with resuspension buffer and mixed well. One microliter of this solution was added to 19 μl resuspension buffer in a new 0.3ml PCR plate and mixed. This new plate was utilised for the “Enrich DNA Fragments” step to create amplified test libraries to guide PreCapture LMPCR with the remaining 20 μl. Precapture LMPCR and QIAquick PCR Purification Kit (Qiagen) were performed as described by the NimbleGen SeqCap EZ Library SR User’s Guide V3.0. To test LMPCR yields K562 biological replicate 3 libraries were amplified for 8, 9 or 10 cycles, quantified on the bioanalyzer and then pooled. K562 biological replicate 1 and 2 libraries were thus amplified for 9 cycles and the yield quantified by bioanalyzer. Capture hybridization was modified from the NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery V3.2. The NimbleGen Hybridization System was set to 42°C and allowed 3 h to equilibrate. Equal nanograms of library from each K562 biological replicate were pooled, some of pooled library was allocated for pre-capture sequencing and 1ug of the pooled library utilized for capture. The library for capture was mixed with 300 µg human Cot-1 DNA (Invitrogen) and 3.34 µl 100 μm TS-INV-HE (hybridisation enhancing) Index Oligos (IDT) to each index adaptor plus 1 µl 1000 μm TS-HE Universal Oligo 1 (IDT) in a 1.5 ml tube. Lid of tube was pierced with an 18 gauge needle and the sample dried at 60 °C in a vacuum concentrator. Once dry the tube was given a new lid to prevent contamination through the needle hole. Library/Cot/Oligo mix was resuspended in 11.2 µl of nuclease and nucleic acid free water, vortexed for 10 s and centrifuged at max speed for 10 s. Sample was solubilised at 70 °C for 10 m before repeating vortexing and centrifugation. Nimblegen 2 x SC Hybridization Buffer (18.5 µl) and SC Hybridization Component A (7.3 µl) were added and vortexing and centrifugation repeated. Sample was denatured at 95°C for 10 m. During this time the “Prepare Mixers” procedure from the NimbleGen Arrays User’s Guide was performed with the omission of the compressed gas step. After denaturation samples was vortexed for 10 s, centrifuged at max speed for 10 s and incubated at 42°C until ready to load onto the NimbleGen Hybridization system. The ‘Load and Hybridize Samples’ procedure from the NimbleGen Arrays User’s Guide was performed to begin array hybridization. Hybridization was conducted for ~3 days. The NimbleGen Arrays User’s Guide protocol was followed to prepare the elution chamber, disassemble, wash and elute the captured DNA from the microarray, with the following modifications. Gasket and elution chamber was setup in a DNA-free laminar flowhood. All washes were conducted with 50 ml buffer in 50 ml falcon tubes. Minelute purification (Qiagen) was conducted using a microfuge. Captured DNA was recovered with two 30 µl elutions from a Minelute column and the final volume adjusted to 60 µl. Post-capture LMPCR and cleanup was performed similar to the NimbleGen SeqCap EZ Library SR User’s Guide V3.0, with the following modifications. LMPCR was run using 5x Phusion buffer for 17 cycles. Each PCR contained 70 µl of master mix and 30 µl of captured DNA. Quantity and quality of amplified captured DNA was determined by bioanalyzer. Enrichment of captured transcripts was measured by qPCR using SYBR Green PCR Master Mix and real time cyclers (Applied Biosystems). Enrichment was determined by the ratio of transcript abundance between the pre and post capture samples using equal nanograms of each. Enrichment was determined for three Nimblegen capture controls and 3 sequences captured specifically by the branchpoint array. Two transcripts not targeted by the capture array were also tested to examine the specificity of capture. Concentrations and volumes were as per the NimbleGen SeqCap EZ Library SR User’s Guide V3.0. Precapture and post capture samples (3 K562 biological replicates) were each sequenced on a single lane of an Illumina® HiSeq.

value: Spleen


title: Trachea RUN2 L008

source_name: Trachea

value: Trachea


title: Thyroid RUN2 L008

source_name: Thyroid

value: Thyroid


title: Thymus RUN2 L008

source_name: Thymus

value: Thymus


title: Testes RUN2 L008

source_name: Testes

value: Testes


title: Prostate RUN2 L007

source_name: Prostate

value: Prostate


title: Intestine RUN2 L007

source_name: Intestine

value: Intestine


title: Ovary RUN2 L007

source_name: Ovary

value: Ovary


title: Maternal Kdm1a mutant 2C embryo rep1

city: Bethesda

first: Todd

last: Macfarlan

address: 6 Center Drive, Building 6B, Room 2B-211

institute: NIH

data_processing:
For expression analysis, only first mate pair was used and reads were trimmed from 3' end to 50bp
Trimmed reads were filtered to a minimum average base quality of 15. We combined the knownGene, ensGene and refGene annotations for mm10 (downloaded from UCSC Genome Browser) with the full RepeatMasker annotation, also from UCSC Genome Browser, to build a single gene annotation.  Redundant transcripts were filtered out using the gffread utility packaged with Cufflinks.  The annotation was modified to include a common gene_id value for same-name repeat elements resulting in a total of 875 repeats.  Sequences for all annotated features were extracted from the mouse genome and RNA-Seq reads were aligned to them using BBMap with 95% identity, up to a single INDEL and up to 2000 equally best alignments per read.
Alignments to features were quantified by counting hits to gene loci and down-weighting read alignments that mapped to multiple gene loci by 1/N^2 where N is equal to the number of gene loci.  Reads aligned to repeat elements were counted in the same way but instead of using gene loci the repeat name was used for binning hits. If a read mapped to multiple repeat features all of the same name then it was counted as 1 hit to that repeat name.
Raw read counts were loaded into R and median normalized for differential expression analysis. For each pair-wise test genes with raw counts less than 10 in all conditions were not tested. Differential expression was performed by testing the null hypothesis that a gene's fold change between conditions is zero. The observed dispersion-mean relationship was fit using a method similar to that of DESeq and the predicted dispersions were used as the minimum dispersion per gene. Fold-changes between conditions were tested by monte-carlo simulation using the observed and estimated means and dispersions to generate random negative binomial distributed count values (the rnbinom method in R).  In each monte-carlo iteration N samples were simulated per condition (N = to the number of samples in each condition), averaged into conditions and the log fold-change was calculated. The resulting simulated log fold-change distributions are normally distributed. Z-scores were computed for each observed log fold-change compared to its corresponding monte-carlo simulated fold-change distribution and translated to two-tail p-values against the normal probability distribution. Raw p-values were adjusted using the Benjamini & Hochberg correction.  Genes and repeats were tested together and marked significant if the adjusted p-value was less than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: .xls files, chrom: chromosome name/number in Ensembl language  gene_id: custom gene id value for the merged annotation  gene_name: gene symbol / repeat name  isRepeat: binary value. 1 = repeat element, 0 = gene  repClass, repFarmily: additional information for repeats or '-' for genes  a: average normalized count for condition a (second condition name in the file name)  b: average normalized count for condition b (first condition name in the file name)  fc: log2 fold change of b / a  tested: binary field indicating if the gene/repeat was tested in DE analysis. based on raw count level (see analysis description)  fc_prob: non-parametric probability derived from monte-carlo log fold-change distribution  pval: p-value from normal distribution  qval: Benjamini & Hochberg adjusted p-values (calculated over those with tested == 1)  significant: yes/no based on qval < 0.05

source_name: 2C embryo

growth_protocol: LSD1 FL/FL mice (From Wang et al, Nature 446, 2007 ) were crossed with ZP3::Cre mice (Jax labs strain 003651) and backcrossed again to generate LSD1 FL/FL, ZP3Cre+ females. . For 2C embryos, these females were crossed with wild type CB6 males

extract_protocol:
NugenPrelude  Direct Lysis buffer, followed by Ovation RNA-seq V2 for cDNA creation, and amplfication, using random hexamer and polydt priming
Tru-seq, amplified cDNA was fragmented with Covaris, and Tru-seq library construction kit was used, beginning with end repair step

treatment_protocol: Litters of 2C embryos were collected at E1.5 and lysed in Prelude direct lysis buffer

value: 2C embryo

value: maternal Kdm1a mutant


title: Muscle RUN2 L007

source_name: Muscle

value: Muscle


title: Maternal Kdm1a mutant 2C embryo rep2


title: Colon RUN2 L005

source_name: Colon

value: Colon


title: MBD3_f_-_IPS_H3K27ac

city: Rehovot

first: Asaf

last: Zviran

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: peaks.bed files were generated using  MACS version 1.4.1, representing enriched peaks.

source_name: MBD3flox/- iPSC

growth_protocol: ESCs, iPSCs, and 4-8 day DOX induced cells were expaned in N2B27 15% KSR  2i/LIF mouse ESC media;  MEF cells in DMEM + 15% FBS

extract_protocol:
Approximately 25*10^6 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature (RT)), and then quenched with glycine (5 min at RT). Fixed cells were lysed in 50mM HEPES KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4°C (Roche, 04693159001), centrifuged at 950 x g for 10 min and re-suspended in 0.2% SDS, 10mM EDTA, 140mM NaCl and 10mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at -4°C to a size range between 200 and 800 bp, and precipitated by centrifugation. 10 ug of antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 hours at room temperature. Washed beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65°C. Eluate was incubated in 65°C for 4 hours, and then treated sequentially with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for two hours. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881).
120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.

treatment_protocol: DOX induction at day 0 at the relevant plate in final concentration of 2ug/ml

value: MBD3flox/- mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming

tag: stage in reprogramming

value: iPSC

value: H3K27ac (ab4729, Abcam)


title: MBD3_-_-_ES_H3K27ac

source_name: MBD3-/- ES

value: MBD3-/- mouse Embryonic Stem Cell (ESC)

value: ES

tag: chip antibody


title: MBD3_f_-_IPS_Oct4

value: Oct4 (sc5279(C-10), Santa Cruz)


title: Cervix RUN2 L005

source_name: Cervix

value: Cervix


title: MBD3_f_-_8day_DOX_Oct4

source_name: MBD3flox/- 8 days after dox induction

value: 8 days after DOX induction


title: MBD3_f_-_8day_DOX_H3K27ac


title: Brain RUN2 L005

source_name: Brain

value: Brain


title: Maternal Kdm1a mutant 2C embryo rep3


title: MBD3_f_-_4day_DOX_Oct4

source_name: MBD3flox/- 4 days after dox induction

value: 4 days after DOX induction


title: Adipose RUN2 L005

source_name: Adipose

value: Adipose


title: WT_IPS_Oct4

source_name: WT iPSC

value: MBD3+/+ mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming


title: MBD3_f_-_4day_DOX_H3K27ac


title: WT_IPS_H3K27ac


title: WT_8day_DOX_H3K27ac

source_name: WT 8 days after dox induction


title: WT_4day_DOX_Oct4

source_name: WT 4 days after dox induction


title: Lung RUN2 L006

source_name: Lung

value: Lung


title: Liver RUN2 L006

source_name: Liver

value: Liver


title: Kidney RUN2 L006

source_name: Kidney

value: Kidney


title: Placenta RUN2 L007

source_name: Placenta

value: Placenta


title: CTRL, 2343-TA-1

source_name: Peripheral whole blood draw, healthy control

value: peripheral whole blood

value: healthy


title: WT_MEF_Oct4

source_name: WT MEF

value: Before DOX induction


title: MBD3_f_-_MEF_Oct4

source_name: MBD3flox/- MEF

value: MBD3flox/- mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming


title: MBD3_f_-_MEF_H3K27ac

value: H3K27ac (ab4729, Abcam)


title: WT_4day_DOX_H3K27ac


title: WT_MEF_H3K27ac


title: GRHL2_ChIPSeq

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 2.1.0 with default configurations.
Duplicates were tagged using Picard Tools' MarkDuplicates.
Peaks were called using MACS version 1.4.2 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file with peaks generated by MACS; Scores represent MACS peaks score.

source_name: placenta tissue embryonic day 17.5 (E17.5)

extract_protocol:
Twenty-five C57BL/6 E17.5 mouse placentas were harvested, maternal uterus tissue was removed and placentas were pooled. Cross-linking was performed with 1% formaldehyde in PBS for 15 min at room temperature. Chromatin was fragmented to an average size of 300-500 bp by sonication. 100 μg chromatin and 5 μg GRHL2 antibody or isotype control antibody (rabbit IgG) as background control were used per assay using a Chromatin Immunoprecipitation Assay Kit (Upstate, Millipore) according to the manufacturer’s protocol.
Libraries of 250-350 bp were prepared for sequencing according to standard Illumina's instructions.

tag: strain

value: placenta

tag: age

value: embryonic day 17.5 (E17.5)

value: wild-type

value: anti-Grhl2 (Sigma Aldrich, catalog# HPA004820, lot# A35809)


title: Heart RUN2 L006

source_name: Heart

value: Heart


title: IgG_ChIPSeq

value: anti-IgG (Jackson ImmunoResearch, catalog# 011-000-003, lot# 79330)


title: dnRaraTh1_Input

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

description: Input

data_processing:
ChIP-seq reads were aligned to the mouse (mm10) genome assembly using Novoalign version 2.07.11 with (-g 65 -x 7) and the output written in SAM format. The SAM format was subsequently converted to BAM format with samtools
The aligned reads were subjected to quality control by omitting reads with mapping quality <10 using samtools and removing the PCR duplicates using picardtools ansd finally converted to BED format for peak calling
Peaks were called using MACS version 2.0.10 with the following settings
MACS: --keep-dup=all -B --SPMR --nomodel --extsize=220 -q 0.1
In the case of H3K4me1, --broad setting was applied to combine nearby significantly enriched regions
Genome_build: mm10
Supplementary_files_format_and_content: Read density files in bigWig format. The read density files were initially produced as bedGraph format, subtract the "input" signal and then finally coverted to bigWig format using “bedGraphToBigWig” utility from UCSC tools. These files contain amplitude of the ChIP-seq signal as number of reads normalized to tags per million reads. Only intensities greater than "input" were reported.

source_name: primary CD4+ T cells from spleen

growth_protocol: Control and dnRara expressing naïve CD4+CD25negCD44loCD62Lhi T cells were isolated by flow cytometry. Cells were cultured with T-cell depleted irradiated splenocytes with anti CD3 (10ug/ml), IL-2 (100U/ml), IL-12  (10ng/ml) and anti IL-4 (10ug/ml) for 3 days followed by IL-2 (50U/ml) for 3 days.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. An aliquot of chromatin (15 ug for H3K4me3 and 25 ug for H3K4me1; 30 ug for all others) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using the antibodies listed. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs using the Apollo 324 system (WaferGen). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.

treatment_protocol: Dead cells were removed using a dead cell removal kit (Miltenyi Biotec)

value: dnRara

value: in vitro polarized T helper1 cells for 6 days

tag: passages

value: FACS sorted naive CD4+T cells cultured in vitro for 6 days


title: Bladder RUN2 L005

source_name: Bladder

value: Bladder


title: Pbmc RUN1 NA

source_name: Pbmc

value: Pbmc


title: dnRaraTh1_H3K4me1

description: Chromatin IP against H3k4me1

value: anti-H3K4me1 (Active Motif 39287)


title: dnRaraTh1_H3K27Ac

description: Chromatin IP against H3k27ac

value: anti-H3k27ac (Active Motif 39133)


title: dnRaraTh1_p300

description: Chromatin IP against p300

value: anti-p300 (Santa Cruz sc–551X)


title: dnRaraTh1_H3K4me3

description: Chromatin IP against H3K4me3

value: anti-H3K4me3 (Active Motif 39159)


title: Mcf7 RUN1 NA


title: WTTh1_H3K4me3

description: Chromatin IP against H3K4me3

value: Wild Type


title: WTTh1_H3K4me1

description: Chromatin IP against H3k4me1


title: K562 RUN1 NA rep2

description:
biological replicate 2
library strategy: Targeted RNA Sequencing (CaptureSeq)


title: WTTh1_p300

description: Chromatin IP against p300


title: WTTh1_H3K27Ac

description: Chromatin IP against H3k27ac


title: K562 RUN1 NA


title: WTTh1_RARA

description: Chromatin IP against RARa

value: anti-RARa (Diagenode C15310155)


title: Trachea RUN1 L002

source_name: Trachea

value: Trachea


title: Thyroid RUN1 L002

source_name: Thyroid

value: Thyroid


title: Spleen RUN1 L002

source_name: Spleen

value: Spleen


title: Esophagus RUN2 L006

source_name: Esophagus

value: Esophagus


title: Placenta RUN1 L008

value: Placenta


title: Testes RUN1 L002

source_name: Testes

value: Testes


title: Colon RUN1 L007

source_name: Colon

value: Colon


title: Intestine RUN1 L008

source_name: Intestine

value: Intestine


title: Muscle RUN1 L008

source_name: Muscle

value: Muscle


title: Bladder RUN1 L007

value: Bladder


title: Prostate RUN1 L008

source_name: Prostate

value: Prostate


title: Ovary RUN1 L008

source_name: Ovary

value: Ovary


title: Cervix RUN1 L007

source_name: Cervix

value: Cervix


title: Liver RUN1 L001

source_name: Liver

value: Liver


title: Kidney RUN1 L002

source_name: Kidney

value: Kidney


title: Lung RUN1 L002

source_name: Lung

value: Lung


title: Hela RUN1 NA

source_name: Hela

value: Hela


title: Lung RUN1 L001


title: Heart RUN1 L002

source_name: Heart

value: Heart


title: Adipose RUN1 L007

source_name: Adipose

value: Adipose


title: Esophagus RUN1 L002


title: Heart RUN1 L001


title: Kidney RUN1 L001


title: Esophagus RUN1 L001


title: Thymus RUN1 L002

source_name: Thymus

value: Thymus


title: Brain RUN1 L007

source_name: Brain

value: Brain


title: SC_RNA-Seq

first: Tong

last: Chen

address: No 16 Nan-xiao-jie Dong-zhi-men-nei

department: State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica

institute: China Academy of Chinese Medical Sciences

data_processing:
Base-calling were performed using RTA and CASAVA.
Sequenced reads were mapped to mouse genome (mm9) using TopHat (version 2.0.4) with a RefSeq based transcript index given to the option “--transcriptome-index”.
m6A peak-calling were done with in-house softwares by comparing the read abundance between m6A-Seq and RNA-Seq samples of the same loci.
The expression of transcripts were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and estimated by Cufflinks (version 2.0.2).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values and modification status of each transcript for all samples.

source_name: Testicular sertoli cells

growth_protocol: Sertoli cells (SCs) were grown in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using Trizol. Highly purified and intact mRNA was enriched from total RNA and fragmented into ~100 nt fragments. For m6A-Seq, mRNA-fragments were enriched by m6A antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Testicular sertoli cells (SC)


title: iPSC_RNA-Seq

source_name: Induced pluripotent stem cells

growth_protocol: Mouse induced pluripotent stem cells (iPSCs) were cultured in DMEM supplemented with 20% KOSR, 0.1 mM b-mercaptoethanol, 1000 units/ml leukemia inhibitory factor, and 0.1 mM nonessential amino acids.

value: Induced pluripotent stem cells (iPSC)


title: iPSC_m6A-Seq

tag: enrichment antibody

tag: enrichment antibody vendor

value: Synaptic Systems

tag: enrichment antibody cat. #

tag: enrichment antibody lot #


title: NSC_RNA-Seq

source_name: Neural stem cells

growth_protocol: Normal neural stem cells (NSCs) were isolated from E12.5 fetal brain and cultured in 1:1 mix of neurobasal medium and DMEM/F12 supplemented with 1xN2, 1xB27, 25 ug/ml BSA, 1xpenicillin/streptomycin/glutamine, 0.1 mM β-mercaptoethanol, 10 ug/ml insulin, 10 ng/ml EGF, and 10 ng/ml bFGF.

tag: cell type

value: Neural stem cells (NSC)


title: ESC_RNA-Seq

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells (ESCs) were cultured in DMEM supplemented with 20% KOSR, 0.1 mM b-mercaptoethanol, 1000 units/ml leukemia inhibitory factor, and 0.1 mM nonessential amino acids.

value: Embryonic stem cells (ESC)


title: NSC_m6A-Seq


title: SC_m6A-Seq


title: AG3-AS13_10

city: Uppsala

first: Konstantia

last: Gkarmiri

country: Sweden

institute: Swedish UNiversity of Agricultural Sciences

description:
AS13-C genes.fpkm.txt
AS13-C differential expression.txt

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality bases using Nesoni, with a quality cutoff of 20 and discarding reads shorter that 75bp.
Bowtie 2.0 (2.1.0) was used to map the RNA-seq reads to the reference genome and to calculate the mean inner distance between pate pairs, followed by the spliced read sligner TopHat 2.0 (2.0.9).
Cufflinks (2.1.1) assembled transcripts and quantified transcript abundance in terms of fragments per kilobase of exon per million mapped fragments (FPKM). Cuffcompare was used to create two combined.gtf files between S4 and control treatment (S4-control) and between AS13 and control treatment (AS13-control), containing a union of all the transfrags present in each sample. Cuffdiff was used to test for statistically significant differences in transcript expression between 2 comparison pairs using multi-read correction. Differentially expressed genes (DEGs) were identified using the two criteria a) log2 fold-change > 3 and b) q-value (false discovery rate (FDR)) < 0.05.
Genome_build: R. solani AG-3 Rhs1AP reference genome, accession number [GenBank: JATN00000000]
Supplementary_files_format_and_content: The processed files include output from Cuffdiff, following the data processing step using the Tuxedo suite.1) tab-delimited text files include FPKM values of genes for the samples (S4-C), (AS13-C), 2) tab-delimited text files lists the results of the differential expression testing between the samples (S4-C), (AS13-C) for genes.

organism: Rhizoctonia solani AG-3 Rhs1AP

source_name: fungal hyphae

extract_protocol:
Total fungal RNA was extracted 72 hours post-inoculation using the RNeasy Plant Mini Kit (Qiagen). For treatments where the fungus was challenged with the bacteria, RNA was extracted from the zone of interaction (1cm). The peripheral fungal zone was used for RNA isolation in the controls containing only the fungus. RNA integrity was analysed after DNase I treatment (Fermentas, St. Leon-Rot, Germany) by electrophoresis on an Agilent Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies, Santa Clara. CA)  and finally 5000ng – 1ug of total RNA were sent to SciLife Lab, Uppsala and subjected to Illumina® TruSeq sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In-vitro bacterial-fungal dual-culture assays were established in 9cm diameter Petri dish systems containing half strength Potato Dextrose Agar (PDA) medium. A 5-mm diam plug taken from the edge of an actively growing colony of R. solani Rhs1AP was inoculated in the centre of each Petri dish. Fresh cells of S. proteamaculans S4 or S. plymuthica AS13  were streaked in 3-cm length parallel line 3-cm on each side of the fungal plug. Control treatments with fungus only were also set up. The R. solani isolate used was the Rhs1AP AG-3.

tag: isolate

tag: anastomosis group

value: fungal hyphae

tag: treatment

value: S. plymuthica AS13


title: AG3-AS13_8


title: AG3_C5

description:
S4-C genes.fpkm.txt
S4-C differential expression.txt
AS13-C genes.fpkm.txt
AS13-C differential expression.txt

value: Control


title: AG3-S4_1

description:
S4-C genes.fpkm.txt
S4-C differential expression.txt

value: S. proteamaculans S4


title: AG3-S4_2


title: AG3_C10


title: Liver RUN1 L002

value: Liver


title: AG3-S4_8


title: AG3_C2


title: Input for brm clf

status: Public on Mar 09 2015

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

description: Sample 12

data_processing:
Basecalls and quality control and pre-aligned (eland) were performed using Illumina Genome analyzer pipeline
ChIP-seq reads were aligned to the Arabidopsis genome (TAIR10) using BOWTIE version 0.12.7. Only perfect match was allowed. The reads mapped to more than one positions were removed.
the alignments were converted to WIG files using MACS.
The program SICER v1.1 (Zang, et al 2009) was used to identify ChIP-enriched domains (peaks) in histone modification signals.
The quantitative comparisons between WT and brm were performed using the ChIPDiff program.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files

organism: Arabidopsis thaliana

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 16h light/8h dark

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27me3 antibody.
Ten ng of ChIP DNA immuoprecipitated by anti-H3K27me3 antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Genome Analyzer IIx was used for high-throughput sequencing of the ChIP-seq library.

tag: genotype/variation

value: brm clf

value: Seedling

tag: developmental stage


title: Input for clf

description: Sample 11

value: clf


title: Input for brm

description: Sample 10

value: brm


title: H3K27me3_ChIPSeq in brm clf_rep1

description: Sample 7

value: anti-H3K27me3 (Millipore, catalog# 07-449, lot# 1959680)


title: H3K27me3_ChIPSeq in brm clf_rep2

description: Sample 8


title: H3K27me3_ChIPSeq in clf_rep1

description: Sample 5


title: H3K27me3_ChIPSeq in clf_rep2

description: Sample 6


title: H3K27me3_ChIPSeq in brm_rep2

description: Sample 4


title: H3K27me3_ChIPSeq in brm_rep1

description: Sample 3


title: H3K27me3_ChIPSeq in wt_rep2

description: Sample 2

value: wild-type


title: ESC_m6A-Seq


title: H3K27me3_ChIPSeq in wt_rep1

description: Sample 1


title: AG3-AS13_6


title: siFTO-input-rep2

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: siFTO-input

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
For each sample, RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene.
m6A peaks were mapped to the coding sequences (CDS), 5’UTRs, 3’UTRs and introns, in that order by using intersectBed from BEDTools according to the RefSeq gene annotations (Ensembl version 68)(Quinlan and Hall, 2010). Considering that individual m6A peaks often mapped to multiple transcript variants of the same RNA, only one transcript variant with the most exon numbers per gene was used here. Meanwhile, adjacent genes on the genome with overlapping transcripts were discarded to avoid mis-assignment of m6A peaks.
Genome_build: mm10

source_name: Mouse 3T3-L1 cell

extract_protocol:
mRNAs were extracted using biotinylated poly(dT) oligo, followed by further removing of contaminated rRNA using RiboMinus Transcriptome Isolation Kit (K1550-02, Invitrogen). Then mRNAs were fragmented into 100-200nt length and subjected to immunoprecipitation with m6A specific antibody by as previously described approache.
the RNA got from IP was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp.

tag: antibody

value: input

tag: cell line

value: FTO knockdown Mouse 3T3-L1 cell

value: Mouse embryo ﬁbroblast 3T3-L1 pre-adipocytes


title: dKO rep2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000. For each sample reads were mapped against the mouse reference genome (NCBI build 37) using Tophat (version 2.0.6) (Trapnell et al, 2009). TopHat was supplied with a known set of gene models (Ensembl Gene Transfer Format (GTF) file version 66). In order to get per sample gene counts, HTSeq-count was used (Anders et al, 2014). This tool generates absolute counts for every gene that is present in the provided GTF file. Approximately 12-17 million reads were uniquely assigned to the transcriptome.
Genome_build: mouse reference genome (NCBI build 37)
Supplementary_files_format_and_content: tab-delimited text files with absolute genes counts per sample

source_name: mESC

extract_protocol:
Total RNA was extracted using Trizol.
Sequencing libraries were constructed using Illumina TruSeq RNA

value: mESC

tag: genotype

value: dKO


title: dKO rep1


title: siCtrl-input-rep2

description: siCtrl-input

value: normal Mouse 3T3-L1 cell

tag: tissue


title: METTL3 knockdown Mouse 3T3-L1 cell 2

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
m6A regions (m6A peaks) were identified by comparing the read abundance between m6A-Seq and RNA-seq samples of the same loci with a method applied in previous report (Meyer et al., 2012). Briefly, the entire mm10 genome was divided into 25 nt bins and the numbers of both m6A-Seq reads and RNA-Seq reads (used as control) mapped to each bin were counted by BEDTools’intersectBed and compared(Quinlan and Hall, 2010). Bins with statistically enriched m6A-Seq reads compared with the RNA-Seq reads (adjusted p-value <0.01, Fisher’s exact test together with Benjamini-Hocberg procedure) were identified and concatenated adjacently with BEDTools’ mergeBed (Quinlan and Hall, 2010).
Differentially expressed genes between control and  FTO or METTL3 knockdown  samples were determined using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

extract_protocol:
Total RNA was isolated from transiently transfected cells with TRI® Reagent (Sigma). mRNA was extracted using biotinylated poly(dT) oligo, followed by further removing of contaminated rRNA using RiboMinus Transcriptome Isolation Kit (K1550-02, Invitrogen).
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp.

value: METTL3 knockdown


title: siFTO-m6a-rep2


title: normal Mouse 3T3-L1 cell 1

value: control


title: wt rep2

tag: strain

value: wt


title: METTL3 knockdown Mouse 3T3-L1 cell 1


title: Input for wt

description: Sample 9

tag: chip antibody


title: normal Mouse 3T3-L1 cell 3

description: FTO-control

extract_protocol:
Total RNA was isolated from transiently transfected cells with TRI® Reagent (Sigma). mRNA was extracted using biotinylated poly(dT) oligo, followed by further removing of contaminated rRNA using RiboMinus Transcriptome Isolation Kit (K1550-02, Invitrogen).
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-end mode, creating reads with a length of 101 bp.


title: normal Mouse 3T3-L1 cell 2


title: wt rep1


title: FTO knockdown Mouse 3T3-L1 cell

description: FTO-knockdown

value: FTO knockdown


title: D10_m6a

value: D10 day Mouse embryo ﬁbroblast 3T3-L1 pre-adipocytes


title: siFTO-m6a


title: siCtrl-m6a


title: D5_input

value: D5 day Mouse embryo ﬁbroblast 3T3-L1 pre-adipocytes


title: siFTO-input

description: siFTO-input


title: D10_input


title: D5_m6a


title: D2_m6a

value: D2 day Mouse embryo ﬁbroblast 3T3-L1 pre-adipocytes


title: D2_input


title: D0_m6a

value: D0 day Mouse embryo ﬁbroblast 3T3-L1 pre-adipocytes


title: D0_input


title: siCtrl-m6a-rep2


title: D-2_m6a

value: D-2 day Mouse embryo ﬁbroblast 3T3-L1 pre-adipocytes


title: D-2_input


title: RNA-seq WT HP1abg-KD replicate #2

status: Public on Mar 08 2015

city: Tel- aviv

first: Ahuvi

last: Yearim

address: Ramat Aviv

department: Human Molecular Genetics and Biochemistry

institute: Tel-Aviv University

description: processed_data file: Rabg_pool_pre100_SE.miso_summary.txt

data_processing:
We united the replicates. We mapped the pooled Fastq files to the mouse genome (mm10) using Tophat2 (Kim et al., 2013) and Bowtie2 (Langmead and Salzberg, 2012). The MISO tool (Katz et al., 2010) was used to estimate inclusion levels of 14,959 exons using the 'run_events_analysis.py --compute-genes-psi' function, based on the SE.mm10.gff3 MISO dataset of verified alternative exons (Katz et al., 2010). We used a prefilter threshold value of 100 read coverage for MISO calculation of the number of reads in the input BAM that map to each event. Events that did not meet the read coverage thresholds were removed.
processed data files format and content: output of the MISO tool
Genome_build: mm10

source_name: R1 mouse embryonic stem cells

growth_protocol: Cells were cultured in ESC medium (DMEM high glucose, 15% ES cell qualified heat inactivated FBS, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 µM β-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2.28 mM L-alanyl-L-glutamine, and 1,000 U/ml LIF), and grown without MEFs on gelatin-coated plates at 37 °C in a humidified atmosphere with 5% CO2. Media was changed daily.

extract_protocol:
Total RNA was extracted from the cells using TRI reagent (Sigma)
Deep sequencing libraries were prepared using standard Illumina TruSeq library preparation kits. 2 x 101-bp paired-end sequencing was performed using an Illumina HiSeq 2000.

treatment_protocol: Cells were transfected with 60nM+60nM+60nM HP1alpha+HP1beta+HP1gamma siGENOME siRNAs (Dharmacon) using Lipofectamine 2000 (Invitrogen). Following transfection, cells were incubated for 48 hours before RNA extraction.

tag: sirna knock-down target

tag: biological replicate

value: replicate 2 of 2

tag: cell line source

value: ATCC


title: BS-seq WT replicate #1

description: processed_data file: bsSeqBedgraphFiles.tar

data_processing:
We united the replicates. We mapped the pooled Fastq files to the mouse genome (mm10) using the Bismark tool (Krueger and Andrews, 2011) and Bowtie (Langmead et al., 2009) with default settings. CpG methylation was extracted from the mapped data using the 'Bismark methylation extractor' function and converted to Bedgraph files using Bismark's 'myBedConverter' function.
processed data files format and content: tar archive of .wg files (one file for each chromosome). Files are tab delimited text with the following format: chr_position, percent_methylation, methylated_reads, total_reads
Genome_build: mm10

extract_protocol:
see Library construction protocol
Genomic DNA (5 µg) was extracted from the cells using High Pure PCR Template Preparation kit (Roche). The DNA was fragmented using Covaris S2 (duty cycle: 20%, intensity: 5, cycles/burst: 200, time: 60 seconds) in 130 µl low-EDTA TE buffer to 250-300 bp fragment size. Samples were concentrated by centrifugation on a Speedvac at room temperature. End repair, adenylation, and ligation were performed according to the Illumina protocol using Illumina methylated adaptors. Adapter-ligated DNA of 200-240 bp was isolated using 2% E-gels and samples were concentrated on a Speedvac at room temperature. Bisulfite conversion was performed with EZ DNA methylation kit (Zymo Research), and DNA was eluted with 30 µl elution buffer. The eluate was aliquoted for six parallel PCR reactions, yielding six independent libraries from the same biological samples. This reduced the incidence of “clonal” reads, reads that share the same alignment position and likely originate from the same template molecule. PCR was performed using Fast Start High Fidelity PCR system (Roche) using the following thermocycling parameters: 2 minutes at 95 ºC followed by 8 cycles of 30 seconds at 95 ºC, 20 seconds at 65 ºC and 45 seconds at 72 ºC, ending with a final extension of 7 minutes at 72 ºC. The PCR products were pooled and purified using Agencourt AMPure XP (Beckman Coulter), and 2 x 100-bp paired-end sequencing was performed using an Illumina HiSeq 2000.

value: replicate 1 of 2


title: BS-seq WT replicate #2


title: siCtrl-input

description: siCtrl-input

value: input


title: RNA-seq WT HP1g-KD replicate #2

description: processed_data file: Rg_pool_pre100_SE.miso_summary.txt

treatment_protocol: Cells were transfected with 90nM siGENOME HP1gamma siRNA (Dharmacon) using Lipofectamine 2000 (Invitrogen). Following transfection, cells were incubated for 48 hours before RNA extraction.


title: RNA-seq WT HP1b-KD replicate #2

description: processed_data file: Rb_pool_pre100_SE.miso_summary.txt

treatment_protocol: Cells were transfected with 90nM siGENOME HP1beta siRNA (Dharmacon) using Lipofectamine 2000 (Invitrogen). Following transfection, cells were incubated for 48 hours before RNA extraction.


title: RNA-seq WT HP1a-KD replicate #2

description: processed_data file: Ra_pool_pre100_SE.miso_summary.txt

treatment_protocol: Cells were transfected with 90nM siGENOME HP1alpha siRNA (Dharmacon) using Lipofectamine 2000 (Invitrogen). Following transfection, cells were incubated for 48 hours before RNA extraction.


title: RNA-seq WT HP1b-KD replicate #1


title: MNase-seq TKO replicate #3

description: processed_data file: mnaseSeqTkoWigFiles.tar

data_processing:
Fastq files of three biological replicates per each condition were mapped to the mouse genome (mm10) using Bowtie2 (Langmead and Salzberg, 2012) with default settings. We constructed a perl script that calculates a single score for 73 bp from the start of the read, thus creating .wg files containing the marking of a single position as the center of the fragment/nucleosome.
processed data files format and content:  tar archive of .wg files (one file for each chromosome). Files are tab delimited text with the following format: chr_position, number_of_nucleosome_centers
Genome_build: mm10

source_name: Dnmt1/3a/3b triple knockout mouse embryonic stem cells

extract_protocol:
Approximately 40 million cells were cross-linked for 10 minutes in 0.5% formaldehyde. Cross-linking was quenched by addition of 125 mM glycine. Nuclei were purified by re-suspending the pellet in Nuc Buffer (15 mM Tris-HCl, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.025% (v/v) NP-40, 1 mM DTT, 0.1 mM PMSF, protease inhibitors) and incubating on ice for 7 minutes. Cells were layered on a sucrose cushion and centrifuged for 20 minutes at 12,000 g to separate the nuclei from the NP-40 detergent. The supernatant was removed, and the purified nuclei were re-suspended in MNase Digestion Buffer (0.32 M sucrose, 50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF) with 160 units of MNase (Worthington) and incubated at 37 ºC for 10 minutes to achieve a digestion efficiency of ~90% mononucleosomes. The reaction was stopped by addition of 60 µl 50 mM EDTA, 25 µl 5 M NaCl, and 15 µl 20% NP-40 and incubated on a rotator for 1 hour at room temperature to release soluble nucleosomes. The reaction was centrifuged for 5 minutes at 10,000 g, and the supernatant, containing soluble nucleosomes without nuclear debris, was moved to a new tube. Proteinase K and SDS (0.5% final concentration) were added and the reaction was incubated for 16 hours at 65 ºC. DNA was purified using Wizard SV gel and PCR cleanup system (Promega) and eluted with 50 µl PBS. RNase A was added and the reaction was incubated for 2 hours at 37 ºC. The reaction was loaded on a 1.5% agarose gel and the ~150-bp mononucleosome band was excised from the gel and purified using Wizard SV gel and PCR cleanup system (Promega).
Deep sequencing libraries were prepared using standard Illumina ChIP-seq library prep kits and 36bp single-end sequencing was performed using an Illumina Genome Analyzer II.

value: replicate 3 of 3

value: Tsumura, A. et al.; 2006; Genes Cells


title: RNA-seq WT HP1abg-KD replicate #1


title: MNase-seq TKO replicate #2

extract_protocol:
Approximately 40 million cells were cross-linked for 10 minutes in 0.5% formaldehyde. Cross-linking was quenched by addition of 125 mM glycine. Nuclei were purified by re-suspending the pellet in Nuc Buffer (15 mM Tris-HCl, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.025% (v/v) NP-40, 1 mM DTT, 0.1 mM PMSF, protease inhibitors) and incubating on ice for 7 minutes. Cells were layered on a sucrose cushion and centrifuged for 20 minutes at 12,000 g to separate the nuclei from the NP-40 detergent. The supernatant was removed, and the purified nuclei were re-suspended in MNase Digestion Buffer (0.32 M sucrose, 50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF) with 160 units of MNase (Worthington) and incubated at 37 ºC for 10 minutes to achieve a digestion efficiency of ~90% mononucleosomes. The reaction was stopped by addition of 60 µl 50 mM EDTA, 25 µl 5 M NaCl, and 15 µl 20% NP-40 and incubated on a rotator for 1 hour at room temperature to release soluble nucleosomes. The reaction was centrifuged for 5 minutes at 10,000 g, and the supernatant, containing soluble nucleosomes without nuclear debris, was moved to a new tube. Proteinase K and SDS (0.5% final concentration) were added and the reaction was incubated for 16 hours at 65 ºC. DNA was purified using Wizard SV gel and PCR cleanup system (Promega) and eluted with 50 µl PBS. RNase A was added and the reaction was incubated for 2 hours at 37 ºC. The reaction was loaded on a 1.5% agarose gel and the ~150-bp mononucleosome band was excised from the gel and purified using Wizard SV gel and PCR cleanup system (Promega).
Deep sequencing libraries were prepared using standard Illumina ChIP-seq library prep kits and 40bp single-end sequencing was performed using an Illumina Genome Analyzer II.

value: replicate 2 of 3


title: RNA-seq WT replicate #2

description: processed_data file: R1_pool_pre100_SE.miso_summary.txt

extract_protocol:
Total RNA was extracted from the cells using TRI reagent (Sigma)
Deep sequencing libraries were prepared using standard Illumina mRNA-seq library preparation kits. Sequencing of 50-bp single-end reads was performed using an Illumina Genome Analyzer II.


title: MNase-seq WT replicate #2

description: processed_data file: mnaseSeqWtWigFiles.tar


title: RNA-seq WT HP1g-KD replicate #1


title: MNase-seq WT replicate #1

extract_protocol:
Approximately 40 million cells were cross-linked for 10 minutes in 0.5% formaldehyde. Cross-linking was quenched by addition of 125 mM glycine. Nuclei were purified by re-suspending the pellet in Nuc Buffer (15 mM Tris-HCl, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.025% (v/v) NP-40, 1 mM DTT, 0.1 mM PMSF, protease inhibitors) and incubating on ice for 7 minutes. Cells were layered on a sucrose cushion and centrifuged for 20 minutes at 12,000 g to separate the nuclei from the NP-40 detergent. The supernatant was removed, and the purified nuclei were re-suspended in MNase Digestion Buffer (0.32 M sucrose, 50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF) with 160 units of MNase (Worthington) and incubated at 37 ºC for 10 minutes to achieve a digestion efficiency of ~90% mononucleosomes. The reaction was stopped by addition of 60 µl 50 mM EDTA, 25 µl 5 M NaCl, and 15 µl 20% NP-40 and incubated on a rotator for 1 hour at room temperature to release soluble nucleosomes. The reaction was centrifuged for 5 minutes at 10,000 g, and the supernatant, containing soluble nucleosomes without nuclear debris, was moved to a new tube. Proteinase K and SDS (0.5% final concentration) were added and the reaction was incubated for 16 hours at 65 ºC. DNA was purified using Wizard SV gel and PCR cleanup system (Promega) and eluted with 50 µl PBS. RNase A was added and the reaction was incubated for 2 hours at 37 ºC. The reaction was loaded on a 1.5% agarose gel and the ~150-bp mononucleosome band was excised from the gel and purified using Wizard SV gel and PCR cleanup system (Promega).
Deep sequencing libraries were prepared using standard Illumina ChIP-seq library prep kits and 39bp single-end sequencing was performed using an Illumina Genome Analyzer II.

value: replicate 1 of 3


title: RNA-seq WT replicate #1


title: MNase-seq WT replicate #3


title: RNA-seq TKO replicate #1

description: processed_data file: tko_pool_pre100_SE.miso_summary.txt


title: RNA-seq TKO replicate #2


title: CSS57 Input sample

status: Public on Mar 07 2015

city: Sevilla

first: Silvia

last: Picossi

address: Avda. Americo Vespucio 49

department: Instituto de Bioquímica Vegetal y Fotosíntesis

institute: CSIC

description: Total DNA

data_processing:
Libraries were loaded at 8pM concentration into the flow cell using the Cluster Station running recipe v7 with the Single-Read Cluster Generation Kit v4 (all Illumina).
The flow cell was loaded into the Genome Analyzer II and samples were sequenced for 120 nucleotides from a single end using the Sequencing Kit v5 and recipe v8 (all Illumina). Manufacturer’s recommendations were strictly followed.
Illumina sequencing data were pre-processed with the standard Illumina pipeline version 1.5 and sequences were aligned to the Anabaena sp. PCC 7120 genome with the Bowtie software 0.12.5. (Langmead et al., 2009)
The Triform algorithm method (Kornacker et al., 2012) was used to the identify peak regions found in the ChIP sample with respect to the control.To identify the specific peaks found in strain CSS57, the CSS68 (control strain) ChIP data was used as the background for analysis of the CSS57 ChIP data.
A cysfinder analysis was carried out to find a primary motif using the sequences of all the peaks.
Genome_build: Anabaena sp. PCC 7120 genome (http://wiki.annotation.jp/Kazusa:CyanoBase:Anabaena_sp._PCC_7120)
Supplementary_files_format_and_content: Processed data files are in tab-delimited text format. Trifrom.PCC7120.bed contains the location in the chromosome of PCC 7120 of the 142 identified peaks. To view the alignment between peaks and genes, upload the contents of the Triform.PCC7120.bed sheet into a custom track using the "Nostoc sp" browser, available via http://microbes.ucsc.edu. Triform.PCC7120.peaks.txt contains all the information about each of the peak, including the Q-values and the raw coverage of the peaks. Primary motif matches.txt shows the information about the peaks containing sequences which match the consensus sequence found (ATAAN2TTTN2TTAT) in the analysis.

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: Total DNA control (Input)

growth_protocol: Cells of strains CSS57 (All3953-TAP) and CSS68 (control) grown in BG110+NH4+10 mM bicarbonate and bubbled with 1% CO2-containing air were filtered, washed, and resuspended in the same medium without bicarbonate and incubated for 3h with aeration with air (no CO2).

extract_protocol:
DNA was purified using phenol:chloroform extraction followed by ethanol precipitation with ammonium acetate and glycogen. DNA was dissolved in DNAse-free purified water.
ChIP DNA Sample Prep Kit (Illumina)

treatment_protocol: Cells were treated with formaldehyde (1 %, 15 min) and glycine (125 mM, 5 min), and collected. The cells were broken, the DNA was sheared by sonication, and a sample was taken for the control (Input). The extract was incubated with IgG-conjugated dynabeads, and the immunoprecipitated material was eluted at 65 ºC. Crosslinking reversion was carried out at 65ºC for 5h and proteins were eliminated using Proteinase K at 55ºC for 2h.

tag: antibody used

value: TAP-tagged version of protein All3953


title: CSS68 ChIP sample

description: Immunoprecipitated DNA

source_name: ChIP sample

value: IgG

value: TAP-tag under the all3953 promoter


title: CSS57 ChIP sample

description: Immunoprecipitated DNA


title: 45D-③ (110614_EAS74_lane8)

city: Yamaguchi

first: tomoyuki

last: kosaka

address: 1677-1 Yoshida

department: Agriculture

country: Japan

institute: Yamaguchi University

description: TSS-seq K.marxianus 45D-3

data_processing:
library strategy: TSS-seq
The generated sequence tags, which were masked head 2bp (n2Y34) and used 24bp as seed length and remaining 10 bp as extantion length if needed, were mapped onto the Kluyveromyces marxianus genomic sequence using the sequence alignment Programme Eland (Illumina).
Unmapped or redundantly mapped sequences were removed from the data set, and only uniquely mapped sequences without any mismatches were used for further analyses.
TSS-tag counts were divided by the total number of uniquely and perfectly (with no mismatch) mapped TSS-tag to calculate TSS-tag ppm (parts per million).
Genome_build: DDBJ/EMBL/GenBank under accession no. AP012213-AP012221
Supplementary_files_format_and_content: Excel, Quantitative data of transcripts of each genes under culture condtiions, Quantification was described as TSS-tags and TSS-tag ppm (parts per million).

organism: Kluyveromyces marxianus

source_name: TSS-seq K.marxianus 45D

growth_protocol: Cells grown in 100-mL Erlenmeyer flasks in 30 ml YPD medium at 30ºC, 160 rpm for 18 h were inoculated at the initial OD660 of about 1 into sequential batch culture, which was conducted in 300-mL Erlenmeyer flasks with 100 ml YPD at 30ºC or 45ºC under the shaking condition (30D and 45D) or the static condition at 30ºC (30DS) or with 100 ml YPX at 30ºC under the shaking condition (30X). The cells were further cultivated under each condition for 6 h and immediately subjected to RNA isolation. Each culture condition for TSS Seq experiments is under the same condition as Rodrussamee, N. et al. Growth and ethanol fermentation ability on hexose and pentose sugars and glucose effect under various conditions in thermotolerant yeast Kluyveromyces marxianus. Appl Microbiol Biotechnol 90, 1573-1586 (2011).

extract_protocol:
Total RNA from cells was isolated by the hot phenol method as described in Aiba, H. et al. Evidence for two functional gal promoters in intact Escherichia coli cells. J. Biol. Chem. 256, 11905-11910 (1981). These RNA was purified using an RNeasy Midi Kit (QIAGEN) with RNase free DNase I (QIAGEN) according to the manufacturer’s instructions. Transcriptional starting site (TSS) Seq analysis was performed using the extracted total RNA, providing precise information on TSSs and their expression levels in a high-throughput manner as described in Tsuchihara, K. et al. Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res. 37, 2249-2263 (2009). TSS-tag counts were divided by the total number of uniquely and perfectly (with no mismatch) mapped TSS-tags to calculate TSS-tag ppm (parts per million).
Two hundred micrograms of the total RNA obtained was subjected to oligo-capping, with some modifications from the original protocol. Briefly, after successive treatment of the RNA with 2.5 U BAP (TaKaRa) at 37 °C for 1 hour and 40 U TAP (Ambion) at 37 °C for 1 hour, the BAP-TAP-treated RNAs were ligated to 1.2 µg of the RNA oligonucleotide 5’- AAUGAUACGGCGACCACCGAGAUCUACACUCUUUCCCUACACGACGCUCUUCCGAUCUGG-3’ using 250 U T4 RNA ligase (TaKaRa) at 20°C for 3 hours. After DNase I treatment (TaKaRa), polyA-containing RNA was selected using oligo-dT powder (Collaborative). The first strand cDNA was synthesized with 10 pmol random hexamer primer (5’-CAAGCAGAAGACGGCATACGANNNNNNC-3’) using SuperScript II (Invitrogen), with incubation at 12 °C for 1 hour and 42 °C overnight. The template RNA was degraded by alkaline treatment. For PCR, 20% of the first strand cDNA was used as the PCR template. Gene Amp PCR kits (PerkinElmer) were used with the PCR primers 5’-AATGATACGGCGACCACCGAG-3’ and 5’-CAAGCAGAAGACGGCATACGA-3’ under the following reaction conditions: 15 cycles at 94 °C for 1 minute, 56 °C for 1 minute and 72 °C for 2 minutes. The PCR fragments were size-fractionated by 12 % polyacrylamide gel electrophoresis, and the fraction that contained the 150-250 bp fragments was recovered. The quality and quantity of the obtained single-stranded first strand cDNAs were assessed using a BioAnalyzer (Agilent). One nanogram of the size-fractionated cDNA was used for sequencing reactions with the Illumina GAIIx. The sequencing reactions were performed according to the manufacturer’s instructions.

treatment_protocol: no treatment

tag: culture condition

value: 45°C, 20 g/l glucose, 6 h, shaking (160 rpm)


title: RNA-seq TKO HP1abg-KD replicate #1

description: processed_data file: TKOabg_pool_pre100_SE.miso_summary.txt

treatment_protocol: Cells were transfected with 80nM+80nM+120nM HP1alpha+HP1beta+HP1gamma siGENOME siRNAs (Dharmacon) using Lipofectamine 2000 (Invitrogen). Following transfection, cells were incubated for 48 hours before RNA extraction.


title: CSS68 Input sample

description: Total DNA


title: RNA-seq TKO HP1abg-KD replicate #2


title: 45D-② (110614_EAS74_lane7)

description: TSS-seq K.marxianus 45D-2


title: 45D-① (110401_lane8)

description: TSS-seq K.marxianus 45D-1


title: 30X-③ (110614_EAS798_lane8)

description: TSS-seq K.marxianus 30X-3

source_name: TSS-seq K.marxianus 30X

value: 30°C, 20 g/l xylose, 6 h, shaking (160 rmp)


title: 30DS-② (110614_EAS798_lane1)

description: TSS-seq K.marxianus 30DS-2

source_name: TSS-seq K.marxianus 30DS

value: 30°C, 20 g/l glucose, 6 h, static


title: 30DS-① (110401_lane7)

description: TSS-seq K.marxianus 30DS-1


title: RNA-seq WT HP1a-KD replicate #1


title: 30DS-③ (110614_EAS798_lane2)

description: TSS-seq K.marxianus 30DS-3


title: MNase-seq TKO replicate #1


title: 30X-① (110614_EAS798_lane6)

description: TSS-seq K.marxianus 30X-1


title: 30D-② (110624_EAS74_lane7)

description: TSS-seq K.marxianus 30D-2

source_name: TSS-seq K.marxianus 30D

value: 30°C, 20 g/l glucose, 6 h, shaking (160 rpm)


title: 30D-③ (110624_EAS74_lane8)

description: TSS-seq K.marxianus 30D-3


title: 30D-① (110401_lane5)

description: TSS-seq K.marxianus 30D-1


title: 30X-② (110614_EAS798_lane7)

description: TSS-seq K.marxianus 30X-2