title: ChIP-seq_MECs_Input

city: Cheonan

first: Keunsoo

last: Kang

institute: Dankook University

data_processing:
Basecalls performed using the CASAVA software.
Sequenced reads were aligned to the mm9 genome assembly using BWA (Li and Durbin, Bioinformatics, 2009) or Bowtie1 (Langmead et al., Genome biology, 2009) or TopHat (Trapnell et al., Bioinformatics, 2009).
ChIP-seq: The HiSeq 2000 sequence reads (single-end) were aligned to the mouse reference genome (mm9) using Bowtie1 (Langmead et al., 2009). The GAII sequence reads (single-end) were aligned to the mouse reference genome (mm9) using BWA (Li and Durbin, 2009). Total mapped reads per sample were normalized to 10 million using the HOMER program (Heinz et al., 2010).
mRNA-seq: After assessing the quality of sequenced single-end reads by FastQC (http://www.bioinformatics.babraham.ac.uk/project/fastqc), contaminating adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore). The trimmed reads from biological triplicates per each sample were aligned to the mouse reference genome (mm9 assembly) using the TopHat program (Trapnell et al., 2012). Transcript abundance was estimated by means of fragment per kilobase of exon per million fragments mapped (FPKM) using Cufflinks (Trapnell et al., 2012). Rarely expressed genes (below 5 FPKM in samples for comparison) were discarded and FPKM values were converted to z-score. We initially identified differentially expressed genes (DEGs) between samples with an FDR-adjusted P value cutoff (< 0.05) using Cuffdiff (Trapnell et al., 2012). Among non-DEGs, we further defined genes showing 0.1 z-score difference and more than 3-fold changes between samples as DEGs.
Genome_build: MGSCv37
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text file contains FPKM values (normalized expression levels) of genes in each sample.

source_name: MECs, p13, no treatment, input

extract_protocol:
ChIP-seq: Frozen-stored mammary tissues from p13 were broken into powder with mortar and pestle. With MECs, cells were cross-linked with 1% formaldehyde for 10 min at RT. Nuclei were extracted in Farnham lysis buffer (5mM PIPES PH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitor). Antibodies against STAT5 (Santa Cruz Biotechnology, cat# sc-1081; L-20, lot# L2012, 10ug) and H3K4me3 (Millipore, cat# 17-164, lot# JBC1793805, 5ug) were used for ChIP. Active Motif performed ChIP with in-house H3K27me3 antibody using pooled tissues from three individual mice of p13.
Libraries were prepared for sequencing using standard Illumina protocols.

value: outbred

value: mammary epithelial cells (MECs)

value: day 13 of pregnancy


title: 4°C, smRNA

status: Public on Dec 31 2013

type: SRA

city: Kiel

first: Till

last: Bayer

address: Düsternbrookerweg 20

department: Marine Ecology

country: Germany

institute: GEOMAR Helmholtz Centre for Ocean Research

description:
4C
Small RNA

library_source: transcriptomic

data_processing:
Illumina Casava 1.7.0 software was used for basecalling.
Trimming of low 3' ends of small RNA reads and filtering of high-quality reads.
Adapter trimming with cutadapt v1.0 with -a ATCTCGTATGCCGTCTTCTGCTTG -g CGACAGGTTCAGAGTTCTACAGTCCGACGATC -O 4.
Small RNA reads were assembled with Velvet (kmer =25) and searched with blastn (-max_target_seqs 5 -outfmt 5) against NCBI nt (11/2012) and the Symbiodinium transcriptome, contigs/reads matching known ncRNA were removed.
Remaining small RNA reads were used for miRNA prediction with miRDeep2 with default parameters.
Supplementary_files_format_and_content: A tab-delimited text file containing short reads and their number of occurences in the dataset.

molecule: total RNA

organism: Symbiodinium sp. A1

source_name: Cold shock culture

growth_protocol: Cultured at 23°C in f/2 medium (Guillard and Ryther 1962) on a 12h/12h day/night regime (daytime: 6 am to 6 pm; night-time: 6 pm to 6 am, light intensity 80 μmolm-2s-1). Salt content in the medium was set to 40 g/l.

extract_protocol:
Cells were frozen in liquid nitrogen, ground with silica beads, and the mirVana miRNA Isolation Kit (Ambion, Austin, TX) was used for extraction of miRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cold shock (4°C for 4 hours), cold stress (16°C for 4 hours), heat stress (34°C for 12 hours), heat shock (36°C for 4 hours), hyposalinity (20 g/L NaCl salt content for 4 hours), hypersalinity (60 g/L NaCl salt content for 4 hours), dark stress (24 hour dark period), dark cycle (12h/12h night/night, sampled at midnight), or control (12h/12h night/night, sampled at noon).

tag: treatment

value: 4°C for 4 hours


title: WT Rep1

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

country: USA

institute: Beckman Research Institute of City of Hope, Center for Informatics

description: Sample 9

data_processing:
Basecalls and barcode analysis were performed using CASAVA version 1.7
Sequenced reads were mapped to mm9 whole genome using rnaseq alignment tool tophat 1.3.1 (bowtie ver 0.12.7) with parameters --max-insertion-length 10 --max-deletion-length 10 --segment-length 20. Other configuarions were kept default.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genome Suite ver 6.12.0713. An expectation/maximization algorithm was used to determine relative isoform abundance levels, and the isoform abundance counts were summarized to the gene level for normalized gene expression abundance counts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (normalized gene expression abundance counts)

organism: Mus musculus

source_name: WT_myeloid cells

growth_protocol: Freshly isolated primary myeloid cells without in vitro culture.

extract_protocol:
CD11b-positive tumor-infiltrating myeloid cells were enriched using specific antibodies and magnetic bead isolation (StemCell Technologies). The total RNA was isolated by using miRVana™ kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Subcutaneously implanted tumors were locally irradiated at 15 Gy and harvested four days later.

tag: strain background

tag: genotype/variation

value: Wild Type (WT)

tag: cell type


title: Noon, mRNA

description:
Noon
PolyA RNA

data_processing:
Illumina Casava 1.7.0 software was used for basecalling.
Reads were mapped against the transcriptome assembly using bowtie 2.2.0 with the parameters -a -t --no-unal --rdg 6,5 --rfg 6,5 --score-min L,-.6,-.4 --no-discordant --no-mixed -p 7 --phred64 --fr.
Output was converted to bam and sorted using Samtools 0.1.15.
Reads were counted using eXpress 1.3.0.
Genome_build: Transcriptome assembly using the same data.

source_name: Control culture

extract_protocol:
Cells were frozen in liquid nitrogen, ground with silica beads, and the mirVana miRNA Isolation Kit (Ambion, Austin, TX) was used for extraction of mRNA (and miRNA, but data separate from this set).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: 12h/12h night/night, sampled at noon


title: TLR9KO Rep4

description: Sample 8

source_name: TLR9KO_myeloid cells

value: TLR9-/- (TLR9KO)

value: CD11b-positive tumor-infiltrating myeloid cells


title: TLR9KO Rep2

description: Sample 6


title: DS, mRNA

description:
DS
PolyA RNA

source_name: Dark stress culture

value: 24 hour dark period


title: TLR9KO Rep3

description: Sample 7


title: 60g, mRNA

description:
60g
PolyA RNA

source_name: Hypersalinity culture

value: 60 g/L NaCl salt content for 4 hours


title: TLR9KO Rep1

description: Sample 5


title: STAT3KO Rep4

description: Sample 4

source_name: STAT3KO_myeloid cells

value: STAT3-/- (Stat3KO; MxCre/Stat3flox)


title: 20g, mRNA

description:
20g
PolyA RNA

source_name: Hyposalinity culture

value: 20 g/L NaCl salt content for 4 hours


title: STAT3KO Rep3

description: Sample 3


title: STAT3KO Rep2

description: Sample 2


title: 36°C, mRNA

description:
36C
PolyA RNA

source_name: Heat shock culture

value: 36°C for 4 hours


title: 34°C, mRNA

description:
34C
PolyA RNA

source_name: Heat stress culture

value: 34°C for 12 hours


title: STAT3KO Rep1

description: Sample 1


title: 16°C, mRNA

description:
16C
PolyA RNA

source_name: Cold stress culture

value: 16°C for 4 hours


title: 4°C, mRNA

description:
4C
PolyA RNA


title: DXB_Male

status: Public on Dec 30 2013

city: Los Angeles

first: Luz

last: Orozco

address: 610 Charles Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
RRBS from mouse liver genomic DNA
DBA/2JxC57BL/6J Male

library_source: genomic

data_processing:
Alignment using BS-Seeker v1, allowing for 5 mismatches
Sort reads as polymorphic on non-polymorphic based on SNPs from C57BL/6J and DBA/2J strains
Genome_build: mm9
Supplementary_files_format_and_content: Columns of ".mapping.summarized" files are: 1)Chromosome, 2)Basepair, 3)Context, 4)Polymorhpic_Nonpolymorphic, 5)Counts_not_methylated, 6)Counts_methylated, 7)%Methylation
Supplementary_files_format_and_content: Columns of "Allele_specific_methylation.txt" are: 1)Chromosome, 2)Base_pair, 3)Mean_%Methylation_B6, 4)StdDev_%Methylation_B6, 5)Mean_%Methylation_DBA, 6)Std_%Methylation_DBA, 7)Delta_%Methylation_B6_and_DBA, 8)Ttest_p-value
Supplementary_files_format_and_content: Columns of "Sex_specific_methylation.txt" are: 1)Chromosome, 2)Basepair, 3)Mean_%Methylation_Females, 4)StdDev_%Methylation_Females, 5)Mean_%Methylation_Males, 6)StdDev_%Methylation_Males, 7)Delta_%Methylation_Females_and_Males, 8)Ttest_p-value
Supplementary_files_format_and_content: Columns of "Binomial_test" files are: 1)Chromosome, 2)Basepair, 3)phat_B6_female, 4)Confidence_interval_lower_bound_B6_female, 5)Confidence_interval_upper_bound_B6_female, 6)phat_DBA_female, 7)Confidence_interval_lower_bound_DBA_female, 8)Confidence_interval_upper_bound_DBA_female, 9)Delta_%Methylation_(B6_female-DBA_female), 10)Absolute_delta_%Methylation

molecule: genomic DNA

source_name: liver, DBA/2JxC57BL/6J Male

extract_protocol:
DNA extraction from liver using phenol-chlorophorm
RRBS protocol using MspI restriction enzyme and Meissner et al. protocl (Nucleic Acids Res 33: 5868-5877, 2005)

tag: strain

tag: gender

value: Male

tag: tissue

value: liver


title: DBA_Male

description:
RRBS from mouse liver genomic DNA
DBA/2J Male

source_name: liver, DBA/2J Male


title: BXD_Male

description:
RRBS from mouse liver genomic DNA
C57BL/6JxDBA/2J Male

source_name: liver, C57BL/6JxDBA/2J Male


title: BXD_Female

description:
RRBS from mouse liver genomic DNA
C57BL/6JxDBA/2J Female

source_name: liver, C57BL/6JxDBA/2J Female

value: Female


title: DBA_Female

description:
RRBS from mouse liver genomic DNA
DBA/2J Female

source_name: liver, DBA/2J Female


title: microRNAs from MD lymphoma from liver

city: Beijing

first: Ling

last: Lian

address: Room 129, Animal Science Department, 2nd Yuanmingyuan West Road, Haidian District

country: China

institute: China Agricultural University

description: microRNAs from MD lymphoma from liver

data_processing: The raw sequenced sequences (sequ-seqs) were subjected to Illumina pipeline filter (Solexa 0.3). Each of the pipeline filter treated data set was further processed with ACGT101-miR, including classify unique sequence family, adapter (ADT) dimmer (5' ADT, 3' ADT & 5' ADT and 3'ADT hooked together without insertion) filter, junk (80% of A, or C, or G, or T, or 3N; 10 repeat of dimmer, 6 repeat of trimmer, or 5 repeat of tetramer; 7 consecutive A, 8 consecutive C, 6 consecutive G or 7 consecutive T; contained only A and C or only G and T) filter, length filter (<16 nt or > 26 nt were removed), simple sequence ( 80% of A, or C, or G, or T, or 3N) filter, low copy (< 3) filter, mRNA, RFam & repbase filter (unique seqs were blasted against mRNA, RFam & repbase. If a unique sequence hits any of the mRNA, or RFam & repbase with 1 error allowed, it was filtered out). After a series of filtering, the remaining sequences (we called mappable sequences) were blasted to miRBase 16.0 and genome (chicken (WUGSC 2.1/galGal3, May 2006) and MDV(AF147806.1)) to identify known and novel miRNAs. Length variation at both 3' and 5 ends and one mismatch inside of the sequence were allowed in alignment.

organism: Gallus gallus

source_name: MD lymphoma from liver

growth_protocol: One hundred and fifty day-old chickens from White Leghorn specific pathogen free line (BWEL) were randomly divided into two groups. One hundred chickens were treatment group and the other 50 were controls. The two groups were kept in seeprate cages with the same filtered-air, positive-pressure condtion, and provided with water and commercial feed ad libitum.

extract_protocol: Total RNA of four samples was extracted using mirVana miRNA Isolation Kit (Ambion, Austin, USA) according to the manufacturer's protocol. Briefly, 10 Î¼g of RNA sample was size fractionated with YM-100 column (Millipore). The larger RNA fraction (>100 KDa) was removed. The smaller RNA fraction (<100KDa) was further fractioned on a 15% tris-borate-EDTA (TBE) urea polyacrylamide gel and 15-50nt fraction was obtained. Subsequently, 5' and 3' RNA adapters were ligated to the small RNA by T4 RNA ligase (Promega), followed by reverse transcription and PCR products purification. Purified products were quantified on the TBS-380 mini-fluorometer (Turner Biosystems) using Picogreen? dsDNA quantitation reagent (Invitrogen) and diluted to 10 nM and transferred for sequencing on the Illumina/Solexa G1 sequence (Illumina, San Diego, USA ).

treatment_protocol: One hundred chickens from treatment group were infected intraperitoneally with 2000 PFU of the MDV GA strain (passage 9) and fifty chickens from controls were injected with the same dosage of diluent (0.2 mL) as controls at one day old. The two groups were kept in separate isolators in different room. The whole trial period lasted to 56 days postinfection (d. p. i.). During this phase, we observed the chicken' clinical signs 2-3 times daily and chose the dying ones to euthanize. Spleen, liver, and lymphocytes isolated from peripheral blood were collected. Meanwhile, chickens from age-matched control were disposed in the same way. All tissues and lymphocytes were immediately stored in RNAfixer  at 4â overnight and transferred to -80â until RNA isolation. Finally, we chose four samples, including uninfected spleen and lymphocytes from control and lymphoma in liver and tumorous spleen from MDV-infected chickens to perform high-throughtput solexa deep sequencing.

tag: breed

value: Specific pathogen free White Leghorn (BWEL)

tag: tissue-type

value: Lymphoma from liver

tag: development stage

value: 46 days post infection


title: DC, mRNA

description:
DC
PolyA RNA

source_name: Dark cycle culture

value: 12h/12h night/night, sampled at midnight


title: DXB_Female

description:
RRBS from mouse liver genomic DNA
DBA/2JxC57BL/6J Female

source_name: liver, DBA/2JxC57BL/6J Female


title: B6_Female

description:
RRBS from mouse liver genomic DNA
C57BL/6J Female

source_name: liver, C57BL/6J Female


title: microRNAs from non-infected lymphocytes

description: microRNAs from non-infected lymphocytes

source_name: non-infected lymphocytes

value: Lymphocytes of peripheral blood

value: 40 days post infection


title: microRNAs from MDV-infected tumorous spleen

source_name: MDV-infected tumorous spleen

value: Spleen


title: microRNAs from non-infected spleen

description: microRNAs from non-infected spleen

source_name: non-infected spleen


title: Untagged, 4.5h in SPM

status: Public on Dec 27 2013

city: Vienna

first: Franz

last: Klein

address: Dr. Bohrg. 9

department: Chromosome Biology

country: Austria

institute: University of Vienna, MFPL

data_processing:
Standard Illumina software was used for basecalling.
We used NextGenMap (http://cibiv.github.com/NextGenMap) for fast and sensitive alignment to the yeast genome version R64-1-1 (S288C).
Read depth per position was generated in Java, dividing each hit by the number of genome-wide matches in case of multi-mapping reads.
All subsequent analyses were performed using R (version 2.15.2). After summing up the read depth of both strands, gaps were filled up with zeros, followed by smoothing with ksmooth (Nadaraja-Watson kernel) with bandwidths as indicated and a resolution of 10bp.
Samples were normalized relative to their negative control (untagged) using NCIS, and the negative control was subtracted from the ChIP files.
Genome_build: R64-1-1
Supplementary_files_format_and_content: Processed data files are tab-separated text files, consisting of 5 columns with headers (mmr in the filenames indicates Million Mapped Reads): [1] Chromosome (1-16), [2] Position (steps of 100), [3] negative control (untagged, smoothed bw=500), [4] ChIP (smoothed bw=500, NCIS normalized), [5] ChIP (negative control subtracted).

organism: Saccharomyces cerevisiae SK1

source_name: meiotic cells, 4.5h in SPM, untagged

growth_protocol: For synchronous sporulation in liquid culture, strains were grown at 30°C overnight in SPS pre-sporulation media (0.5% Difco yeast extract, 1% Difco peptone, 0.17% Difco yeast nitrogen base w/o AA&AS, 1% potassium acetate, 0.5% ammonium sulphate, 0.05 M potassium-biphthalate, pH 5.5) to an OD660 of 1.1-1.3 (4x10^7 cells/ml). Meiosis was induced by a subsequent wash and transfer of the cells into pre-warmed supplemented SPM (1% potassium acetate, 0.001% PPG2000, 4 mg/L Ura, 4 mg/L Trp, 4 mg/L His, 4 mg/L Arg, 6 mg/L Leu) at equal volume. Maximum aeration was provided for efficient meiosis.

extract_protocol:
ChIP from meiotic cultures was performed as described by Panizza (2011). In brief, 4x10^9 cells were collected per time point and incubated with para-formaldehyde (1% final concentration) for 15 minutes at 25°C. Cross-linking was stopped by addition of glycine to 131 mM. 4x10^9 cells were divided into 8 aliquots and separately opened using a multibead shocker (YASUI-KIKAI, Osaka) at 2,500 rpm, 15 cycles of 30 sec on and 30 sec off, at 4°C. Extracts were sonicated to an average of 200bp by a Covaris S2 instrument. After removing the cell debris, the supernatant was used for the chromatin immunoprecipitation. For each sample, 50 μl Dynabeads Pan mouse IgG (Invitrogen), 50 μl Dynabeads® Pan Mouse IgG (invitrogen) were incubated with the 9E11 anti-myc (mouse) antibody for 6-15 hr at 4°C. The precipitated DNA was used as a template for quantitative real-time PCR using GoTaq qPCR Master Mix for SYBR assay (Promega) (primer sequences are available upon request).
For genome-wide analysis (ChIP-seq), one-tenth of the ChIP DNA was analyzed by real-time PCR (qChIP) while the remaining DNA was concentrated by precipitation in ethanol.
For the preparation of libraries for Illumina sequencing, we strictly followed the protocols provided by Illumina (Illumina ChIP-seq DNA sample prep protocol). Briefly, DNA-ends were repaired to convert overhangs to phosphorylated blunt ends with T4 DNA polymerase, E. coli DNA Pol I (Klenow fragment), and T4 polynucleotide kinase (PNK). An 'A' nucleotide was added to the 3' end of the blunt ended fragments using Klenow fragment (3' to 5' exo minus). This prepared the DNA fragments for ligation to the adapters (Truseq Adaptor1-5) which have a single 'T' base overhang at their 3' ends. After ligation, excess adaptors were removed by selecting a certain size range from 200-500bp with QIAquick Gel Extraction Kit (Qiagen). Purified templates were PCR amplified with 15-18 cycles by KAPA-HiFi Hot Start PCR Kit (KAPA biosystems). Before hybridization to the flow cell, the amount and the size of the DNA library was controlled to be at least 1µg/ul (for an average fragment size of 300bp).

value: YFK1, MAT a/alpha, HO

tag: mutant background

value: wild type

value: meiotic cells

tag: time in spm

value: 4.5 hours

tag: immunoprecipitated protein

tag: chip antibody

value: 9E11, monocolonal mouse anti-Myc


title: Sgs1-myc, 4.5h in SPM

source_name: meiotic cells, 4.5h in SPM, Sgs1-ChIP

value: YFK1701, MAT a/alpha ho::LYS2/=, arg4-Nsp/+, his4X/=, leu2::hisG/=, lys2/=, trp1::hisG/=, ura3/=, SGS1-MYC18::TRP1/=


title: Sgs1-myc, 3.5h in SPM

source_name: meiotic cells, 3.5h in SPM, Sgs1-ChIP

value: 3.5 hours


title: Smc6-myc, spo11delta, 4.5h in SPM

source_name: meiotic cells, 4.5h in SPM, Smc6-ChIP, spo11delta

value: YFK5316, MAT a/alpha ho::LYS2/=, Smc6-Myc13::KanMX/=, ura3/=, spo11∆::hisG::URA3::hisG/=, trp1::hisG/=


title: RNA-seq_Wholetissue_Controlp13-rep2

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

description:
mRNA
Processed data file: virgin_p13_p18_FPKM.txt

source_name: mammary tissues, control, p13, no treatment

growth_protocol: We mated Ezh2f/f mice (Ezhkova et al., 2011; Wang et al., 2010) with the control transgenic mouse line A (Wagner et al., 1997) in order to generate mice with mammary-specific deletion of Ezh2. Ezh1 knockout mice were obtained from Rockefeller University (Ezhkova et al., 2011). Genotyping was confirmed by PCR using DNAs from ear clips or mammary epithelial cells (MECs). All animals were handled and housed in accordance with the guidelines of the National Institutes of Diabetes, Digestive and Kidney Diseses Animal Care and Use Committee.

extract_protocol:
RNA-seq: Poly(A) RNA were purified twice with Trizol and RNeasy® Plus Mini Kit (Qiagen). cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Ten- to twelve-week-old mature virgin female mice were checked for stage of estrous cycle by vaginal cytology and anesthetized at estrus with an intraperitoneal injection of avertin and the left 4th mammary fat pad was collected after removal of the lymph node. Two hours after recovery from anesthesia, PRL (prolactin, 5 μg/g body weight) was injected intraperitoneally. The right 4th mammary fat pads were collected two hours later.

tag: strain/background

value: outbred

value: MMTV-Cre

value: mammary

tag: developmental stage

value: day 13 of pregnancy


title: Smc6-myc, spo11delta, 3.5h in SPM

source_name: meiotic cells, 3.5h in SPM, Smc6-ChIP, spo11delta


title: Term placenta x weeks

status: Public on Dec 28 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

data_processing:
Illumina Casava1.7 software used for basecalling
Read mapping: Rtwo reference sequences were prepared based on the HG19 reference genome
The alignment was performed using the bowtie alignment software version  0.12.8
methylation calls files for C's in the bowtie alignment files were generated using Bismarck software
Genome_build: HG19
Supplementary_files_format_and_content: methylation calls files

organism: Homo sapiens

source_name: normal placenta tissue

extract_protocol:
DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)
BS-seq library constructing, 10ug genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80-100 bp, 100-120 bp to 120-150bp. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50ul consisting of 20ul purified DNA, 4ul 2.5 mM dNTP, 5 ul 10X buffer, 0.5 ul JumpStart Taq DNA polymerase, 2ul 10uM PCR primers and 37.5 ul ÎœltraPure TM Water and the following thermal cycling program: 94C 30 s, 10 cycles of 94C 30 s, 60C 30 s, 72C 30 s then prolong with 1 min at 72C. PCR products were sequenced with an Illumina genome analyzer.

value: normal placenta tissue

tag: disease status

value: Healthy


title: Liver

source_name: normal liver tissue

value: normal liver tissue


title: Brain

source_name: normal brain tissue

value: normal brain tissue


title: Smc6-myc, 3.5h in SPM

source_name: meiotic cells, 3.5h in SPM, Smc6-ChIP

value: YFK2754, MAT a/alpha ho::LYS2/=, Smc6-Myc13::KanMX/=, ura3/=, leu2::hisG/=, trp1::hisG/=


title: P300

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description: single read

data_processing:
Sequence reads were aligned to the hg19 genome using bowtie
Genome_build: hg19
Supplementary_files_format_and_content: peak files

growth_protocol: CUTLL1 cells were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, penicillin and streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to New England Biolabs instructions accompanying the DNA Sample Prep Master Mix Set 1 (NEB E6040S).

treatment_protocol: CUTLL1 cells were treated with vehile (DMSO) or GSI (compound E) for 3 days, and treated with GSI for 3 days following by washing and 4 hours of additional treatement in the absence of GSI

tag: cell line

tag: tumor stage

value: T lymphoblastic leukemia/lymphoma cell line

value: T lymphocyte

tag: treatment

value: vehicle

tag: antibody


title: MED1

description: single read

tag: cell type


title: H3K27ac w4h

description: multiplex

value: GSI 72 hrs, wash out 4 hrs

value: H3K27ac (Abcam ab4729)


title: B6_Male

description:
RRBS from mouse liver genomic DNA
C57BL/6J MALE

source_name: liver, C57BL/6J MALE

tag: strain

tag: gender

value: Male

value: liver


title: Smc6-myc, 4.5h in SPM

source_name: meiotic cells, 4.5h in SPM, Smc6-ChIP

value: wild type

value: meiotic cells

value: 4.5 hours

value: 9E11, monocolonal mouse anti-Myc


title: HEK293 cells transfected with pCag-EGFP_mosIR plasmid.

city: Prague 4

first: Radek

last: Malik

address: Videnska 1083

department: Dep. of Epigenetics Regulations

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
In the first round of mapping, sequence reads of 18-50 nt length (after subtracking the adaptor sequence) were obtained and mapped onto specified plasmid considering only perfectly matched reads.
In the second round of mapping (A>I edited reads), reads not mapped during the first round were re-mapped onto specified plasmid allowing for up to 5 A-to-G mismatches.
Supplementary_files_format_and_content: Columns in processed files containing perfect matches (*_Perfect.txt) are as follows: Sequence = sequence of the particular read mapped; Mapped = number indicating, how many times is the particular read present in the dataset; Strand = indicates if the read was mapped on a sense or an antisense strand of the plasmid; Length = length of the read.
Supplementary_files_format_and_content: Columns in processed files containing A-to_G edited reads (*_Edited.txt) are as follows: Sequence = sequence of the particular read mapped; Mapped = number indicating, how many times is the particular read present in the dataset; Strand = indicates if the read was mapped on a sense or an antisense strand of the plasmid; Length = length of the read; Edited nucleotides = number of A-to-G mismatches present within the mapped read.

source_name: cell line

growth_protocol: HEK293 cells were grown under standard tissue culture conditions (DMEM supplemented with 10% FCS).

extract_protocol:
Total RNA was isolated using RNAzol RT (Molecular Research Center). Further sample processing and SOLiD sequencing was performed by Seqomics Ltd. (Hungary). Briefly, samples were depleted of ribosomal RNA using RiboMinus rRNA Removal Kit, eluted twice int
Sample processing and SOLiD sequencing was performed by Seqomics Ltd. (Hungary). Briefly, samples were depleted of ribosomal RNA using RiboMinus rRNA Removal Kit, eluted twice into 15 ul and treated with DNase I (5 ul 10x DNase I buffer, 2.5 U DNase I and water up to 50 ul reaction) 20 min at 37°C. Samples were ethanol-precipitated, eluted into 10 ul TE buffer and fragmented by RNase III treatment (1 ul 10x RNaseIII buffer, 8 ul sample, 1 ul RNaseIII) 10 min at 37°C. Fragmented samples were precipitated by ethanol and eluted into 4 ul. Adaptor was hybridized and ligated to each sample (10 ul 2x ligase buffer, 2 ul Adaptor mix, 3 ul hybridization solution, 2 ul ligation enzyme) by incubating O.N. at 16°C. Adaptor-ligated RNA was subjected to reverse transcription (4 ul 10x RT buffer, 2 ul dNTP mix, 2 ul RT primer, 1 ul ArrayScript RT, 13 ul water) for 40 min at 42°C. Resulting cDNA was purified using PCR Purification kit (Qiagen) and eluted into 10 ul. cDNA was run on 6% TBE-Urea gel and fragments 150-250 nt in length were excised. Isolated cDNA was amplified for 15 cycles using AmpliTaq DNA polymerase and purified by PCR Purification kit (elution twice in 10 ul). Second round of size selection on PAGE gel was performed and PCR products 110-130 nt in length were excised from gel and isolated.  Purified amplicons were sequenced using Abi SOLiD 4 platform.

treatment_protocol: HEK293 cells were transiently transfected with 3 micrograms of hairpin dsRNA-expressing pCag-EGFP_MosIR or control pCag-EGFP plasmid (per well in a 6-well plate) using TurboFect (Fermentas) transfection reagent.

tag: passages

tag: transfected plasmid


title: HEK293 cells transfected with pCag-EGFP plasmid.

value: pCag-EGFP


title: input DNA w4h

description: single read


title: RBPJ w4h

description: single read

value: Rabbit anti RBPJ


title: input DNA GSI

description: single read

value: GSI 72 hrs


title: RBPJ GSI

description: single read


title: H3K27ac GSI

description: multiplex


title: ETS1

description: paired-end sequencing

value: ETS1 (santa cruz sc-350)


title: NOTCH1 GSI

description: single read

value: Rabbit anti Notch1


title: RUNX1

description: single read

value: RUNX1 (Abcam ab23980


title: GABPA

description: paired-end sequencing

value: T lymphoblastic leukemia/lymphoma cell line

value: GABPA (santa cruz sc-22810)


title: AR Input sample

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
ChIP-seq reads were aligned to the human genome (NCBI build 37 and hg19) using Bowtie version 0.12.8.
Reads with an unique mapped location were used for peak calling by the software MACS (v1.4), using input data as controls.
MACS Peaks with low signals were  removed from the final list.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: BED files containing peak calls

source_name: AR Input sample

growth_protocol: Phenol Red Free, Charcoal Stripped Media for 4 days with 10%CSS

extract_protocol:
Fixation and processing for was carried out as described by others (Goldberg et al., 2010). Immunoprecipitation was carried out with Anti-Androgen Receptor Antibody, PG-21 (Millipore) or Glucocorticoid Receptor Antibody #7437 (Cell Signaling).
Immunoprecipitated DNA was quantified by picogreen and size was evaluated on a HighSense BioAnalyzer chip. Fragments between 100 and 600 bp were collected using an automated system (Pippin Prep, Sage Science) then end repaired, ligated and amplified for 15 cycles using reagents included in the Truseq DNA Sample Preparation kit from Illumina. Experimental conditions followed strictly the instructions of the manufacturer, with the exception of the adaptors being diluted 1/10 for the input DNA and 1/50 for all other samples.

treatment_protocol: 30 minute treatment with DEX (100nM) or DHT (1nM)

value: LREX'

value: Prostate Cancer

tag: phenotype

value: Enzalutamide Resistant


title: GR Input sample

source_name: GR Input sample


title: IP:GR with Dex treatment

source_name: IP:GR with Dex treatment


title: RN2-shDdx5.1322_48hrs on-doxycycline

status: Public on Dec 26 2013

city: Cold Spring Harbor

first: Anthony

last: Mazurek

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: 3 replicates

data_processing:
Paired-end 101 basepair sequencing reads obtained for the same RNA library run on 2 different lanes of the HiSeq2000 were concatenated tail-to-head using the "Concatenate Datasets" python script in Galaxy (Goecks et al. Genome Biology. 2010 August 25;11(8):R86, Blankenberg et al. Current Protocols in Molecular Biology. 2010 January; Chapter 19:Unit 19.10.1-21, and Giardine et al. Genome Research. 2005 October; 15(10):1451-1455). Galaxy was used for all subsequent steps of data processing.
Sequences were mapped to the mouse genome using cannonical mm9 and TopHat software version 1.4.1 with expected (mean) inner distance between mate-pairs of 108 bases.
Differences in transcript abundances between experimental (Ddx5 knockdown) and control (RLuc-713) samples were determined using CuffDiff (with replicates) software version 1.3.0. TopHat results from the sequencing results of the triplicate DDX5 knockdown libraries by a particular shRNA (i.e. shDDX5.1322 or D5-1322) and sequencing results of the triplicate control shRNA (shRen.713 or RLuc-713) libraries at a specific timepoint (i.e. 24hrs of shRNA induction) were given as input for the CuffDiff analysis. Output results from CuffDiff analysis include one value of RPKM per transcript from the triplicate experimental shRNA samples (i.e. D5-1322) at the indicated timepoint (i.e. 24hrs) and one value of RPKM per transcript from the triplicate control shRNA condition (i.e. RLuc-713) at the same timepoint. Parameters used for analysis with CuffDiff included unstranded (standard Illumina) library type, include bias correction, and normalize to total number of mapped reads. Significance threshold was set at q=0.1 and all transcripts with 100 mapped reads or more were included for analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: AML cell line

growth_protocol: RN2 cells were cultured in RPMI 1640 media (Corning CellGro catalog # 10-040-CV) + 10% fetal bovine serum + 1mg/mL G418 + 1µg/mL doxycycline. Each 3.5cm culture was seeded with 400,000 RN2 cells in 4mL of the indicated growth media containing doxycycline at the beginning of the experiment.

extract_protocol:
RNA was extracted from 1,000,000 derivative RN2 cells per culture at either 24 hours or 48 hours of doxycycline treatment using the Qiagen RNeasy Mini Kit (catalog # 74104) as per the manufacturer's instructions that included the recommended on-column Dnase digestion step. RN2 cells were lysed using the Qiagen QIAshredder (catalog # 79654) as per manufacturer's instructions.
RNA libraries were prepared from 0.7µg of each RNA sample using the Illumina TruSeq Stranded Total RNA kit (catalog # RS-122-2201) as per the manufacturer's protocol. The final RNA libraries were barcoded for multiplex sequencing of three separate RNA library pools. For RNA library pool #1 the RNA libraries prepared from replicate #1 cultures of each derivate RN2 derivative cell line at both timepoints of doxycycline treatment were pooled. For RNA pool #2 the the RNA libraries prepared from replicate #2 cultures of each derivative RN2 cell line at both timepoints of doxycycline treatment were pooled. For RNA pool #3 the RNA libraries prepared from replicate #3 cultures of each derivative RN2 cell line at both timepoints of doxycycline treatment were pooled. Each pool was loaded onto two lanes of the Illumina HiSeq2000 sequencer to obtain a sufficient number of sequence reads for each individual RNA library. The following Illumina adaptors were used for barcoding: AR005 - all shDdx5.1322 timepoint 24hrs RNA libraries, AR006 - all shDdx5.2086 timepoint 24hrs RNA libraries, AR012 - all shRen.713 timepoint 24hrs RNA libraries, AR014 - all shDdx5.1322 timepoint 48hrs RNA libraries, AR018 - all shDdx5.2086 timepoint 48hrs RNA libraries, and AR019 - all shRen.713 timepoint 48hrs RNA libraries.

treatment_protocol: Doxycycline was added to each culture at 0 hours in the experiment for a final concentration of 1µg/mL to induce expression of the indicated shRNA.

tag: timpoint shrna induction

value: 48 hours

tag: induced shrna


title: BRD4

description: single read

value: T lymphocyte

value: vehicle


title: RN2-shDdx5.1322_24hrs on-doxycycline

description: 3 replicates

value: 24 hours


title: RN2-shRen.713_48hrs on-doxycycline

description: 3 replicates


title: IP:AR with DHT treatment

source_name: IP:AR with DHT treatment


title: RN2-shRen.713_24hrs on-doxycycline

description: 3 replicates


title: RN2-shDdx5.2086_24hrs on-doxycycline

description: 3 replicates


title: rdp1∆ + Dcr1OE

city: Boston

first: Ruby

last: Yu

state: MA

address: 240 Longwood Avenue

department: Cell Biology

institute: Harvard University

data_processing:
Base-calling was performing using CASAVA-1.8.2
First, reads containing linker sequence and long polyA tracts were removed. Remaining reads were aligned using novoalign (www.novocraft.com) to the S. pombe h- genome, with configurations -l14, -t30, and -r Random.
Reads were then converted to an Integrated Genome Viewer (IGV)-viewable format, mapping the 5' most nucleotide of each small RNA.
Genome_build: S. pombe h- (GCA_000002945.1)
Supplementary_files_format_and_content: IGV-viewable files are tab delimited and include reads per million at each nucleotide position.

organism: Schizosaccharomyces pombe

source_name: rdp1∆ + Dcr1OE_haploid cells

growth_protocol: Cells were grown in minimal media lacking leucine (EMMC-LEU)

extract_protocol:
RNA was extracted using the hot phenol method (Leeds et al., 1991), and small RNAs were purified using the mirVanaTM miRNA Isolation kit (Ambion). These sRNAs were used for library construction.
Small RNA libraries were constructed as previously described (Halic and Moazed, 2010). Briefly, 20-30nt RNA was size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 3’ adapter. The ligated species were size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 5’ adapter. RNA was then reverse transcribed into cDNA and PCR-amplified in a two-step process. Amplified cDNA was gel-purified and sequenced on Illumina High-Seq 2000 platform.

tag: genotype/variation

value: h- ade6-M210 leu1-32 ura4+ rdp1∆::hphMX

tag: transformed with

value: PDM 914 (Dcr1 overexpression construct)


title: rdp1∆ + vector

source_name: rdp1∆ + vector_haploid cells

value: PDM 829 (vector control)


title: dcr1∆+vector

description: barcode: TTAGGC

data_processing:
Basecalls performed using CASAVA-1.8.2
Raw reads were separated by barcode and the first 7 nucleotides (6nt barcode and following 'T') were removed from the reads and attached to the identifier.
Reads were mapped using bowtie with default configurations.
Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV)
Genome_build: GCA_000002945.1
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV) in an IGV-viewable format.

source_name: haploid cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min at room temperature (RT), then quenched with 130 mM glycine for 5 min at RT, harvested by centrifugation, washed twice with TBS (50 mM Tris, pH 7.6,150 mM NaCl), and flash-frozen. Cell pellets were resuspended in 500 ul lysis buffer (50 mM Hepes-KOH, pH 7.5, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% SDS, and protease inhibitors) and disrupted by bead beating (Mini Beadbeater, Biospec products) for 6x30 sec with 1 ml 0.5 mm glass beads. Tubes were punctured and the flow-through was collected in a new tube by centrifugation.  After sonication for 3x20 sec at 40% amplitude (Branson Digital Sonifier), the extract was centrifuged (Eppendorf 5415R) for 15 min at 13000 rpm.  Anti-H3K9me2 antibody (Abcam, ab1220) was pre-incubated with washed Dynabeads Protein A, and for each immunoprecipitation, 2 ug antibody coupled to 30ul beads  was added to 400 ul soluble chromatin, and lysis buffer was added for a final volume of 600 ul. Samples were rotated for 2h at 4°C, the beads were collected on magnetic stands, and washed 3 times with 1 ml lysis buffer and once with 1 ml TE, and eluted with 100 ul pre-heated buffer (50 mM Tris pH 8.0, 10mM EDTA, 1% SDS) at 65°C for 15 min. The eluate was collected and 150 ul 1xTE/0.67% SDS was added. Input and immunoprecipitated samples were incubated overnight at 65°C to reverse crosslinks, diluted with 250 ul TE, and treated with 50 ug RNase A at 37°C for 1h. 60 ug glycogen and 5 ul proteinase K (Roche) was added and incubation was continued at 55°C for 1h. 22 ul of 10M LiCl was added and the samples were extracted with phenol/chloroform, and EtOH precipitated.
Libraries for Illumina sequencing were constructed following the manufacturer’s protocols, starting with ∼5 ng of immune-precipitated DNA fragments. Each library was generated with custom-made adapters carrying unique barcode sequence at the ligating end (Wong and Struhl, 2011). Barcoded libraries were mixed and sequenced with Illumina HiSeq2000.
Barcodes are the first 6 nt of each read and are listed in a column for each of the raw files. Each barcode (the 7th nt) should be followed by a T.

tag: genotype

value: h- ade6-M210 leu1-32 ura4+ dcr1∆::hphMX

tag: strain number

tag: plasmid

value: PDM 829

value: H3K9me2A (bcam, ab1220)


title: H3K27ac DMSO

description: multiplex

tag: cell line

value: H3K27ac (Abcam ab4729)


title: NOTCH1 w4h

description: single read

tag: tumor stage

value: GSI 72 hrs, wash out 4 hrs

value: Rabbit anti Notch1


title: rdp1∆+Ago1OE

description: barcode: GATCAG

value: PDM 817


title: clr4∆+vector

description: barcode: CGATGT

value: h- ade6-M210 leu1-32 ura4+ clr4∆::hphMX


title: dcr1∆+Rdp1OE

description: barcode: TGACCA

value: PDM 936


title: dcr1∆+Ago1OE

description: barcode: CGATGT


title: rdp1∆+Dcr1OE

description: barcode: TAGCTT

value: PDM 914


title: RN2-shDdx5.2086_48hrs on-doxycycline

description: 3 replicates

value: 48 hours


title: rdp1∆+vector

description: barcode: GCCAAT


title: ura4-UTRD+hp cid14∆

description: Sample 3

data_processing:
Base-calling was performing using CASAVA-1.7.0.
First, reads containing linker sequence and long polyA tracts were removed. Remaining reads were aligned using Maq (http://maq.sourceforge. net/) to the S. pombe h- genome.
Reads were then converted to an Integrated Genome Viewer (IGV)-viewable format, mapping the 3' most nucleotide of each small RNA.
The wildtype genome build was modified at the ura4 locus to reflect the ura4-UTRDIS/kanMX (1491A) or ura4-UTRD/kanMX (1491C) genotypes. Fasta files for each of these genomes are included.
The modified genome build 'PombeGenome_1491A.fasta' was used to generate the 1647A_terDISPkan*.igv files
The modified genome build 'PombeGenome_1491C.fasta' was used to generate the following files;
1647C_terKOkan*.igv,
1647C_clr4D_terKOkan*.igv ,
1647C_cid14D_terKOkan*.igv,
1647C_rdp1D_terKOkan*.igv files
The rest of the igv files were generated using wild type genome build.
Genome_build: S. pombe h- (GCA_000002945.1)
Supplementary_files_format_and_content: IGV-viewable files are tab delimited and include reads per million at each nucleotide position.

extract_protocol:
To purify Ago1-associated sRNAs, cells transformed with plasmid pREP1-N3X-FLAG-Ago1 (Buker et al., 2007) were grown in 3L EMMC–Leu to a concentration of 1-2x107 cells/ml, spun down, washed twice in water, and pellets flash-frozen in liquid nitrogen. Cells were resuspended in 1 ml lysis buffer (50mM HEPES pH 7.6, 5mM MgOAc, 0.1 mM EDTA, 0.1 mM EGTA, 300 mM NaOAc, 5% glycerol, 1mM PMSF, 0.25% NP-40, plus Roche Complete Protease Inhibitor Cocktail tablet) per 1g cells in 15 mL tubes. Glass beads (Biospec, >1vol/vol cell suspension, 0.5 mm) were added and cells were disrupted in a FastPrep®-24 homogenizer (MP Biomedicals) at 6.5 meters/second for 3 times 30 s. Tubes were punctured with a 21 gage needle and the flow-through was collected in 50 ml tubes by spinning at 1000 rpm for 2 min. The flow-through was transferred to fresh tubes and spun down in a microfuge (Eppendorf 5415R) at 4300 rpm for 15 min. The supernatant was then transferred to a fresh tube. For each 1 ml supernatant, 15 ul pre-washed M2 anti-Flag resin was added and samples were incubated at 4°C for 2h. The resin was then collected by spinning at 1400 rpm for 1 min (Eppendorf 5415R), washed 3 times with lysis buffer, and once with lysis buffer without NP-40. The washed resin was resuspended in diethyl pyrocarbonate-treated water, and extracted with an equal volume of Phenol/Chloroform/Isoamylalcohol. The aqueous phase was transferred to phase lock tubes and extracted again with Phenol/Chloroform/Isoamylalcohol, precipitated by the addition of 2 volume EtOH, 1/10 volume 3M NaOAc pH 5.2, and 60 ug glycogen, and resuspended in 10 ul H2O.
Ago1-associated small RNA libraries were constructed as previously described (Halic and Moazed, 2010). Briefly, 21-24nt RNA was size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 3’ adapter. The ligated species were size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 5’ adapter. RNA was then reverse transcribed into cDNA and PCR-amplified in a two-step process.
sequencing of Ago1-associated small RNAs

value: h- ade6-M210 leu1-32 ura4-UTRD::kanMX shura4-5/natR cid14∆::hphMX

tag: molecule subtype

value: Ago1-associated siRNA


title: ago1∆+Rdp1OE

description: barcode: ACTTGA

value: h+ leu1-32 ura4-D18 imr1R(NcoI)::ura4+ oriI ade6-216 ago1∆::TAP-KanMX6

value: SPY 120

tag: antibody


title: ago1∆+Dcr1OE

description: barcode: CAGATC


title: ago1∆+vector

description: barcode: GCCAAT


title: ura4-UTRD+hp

description: Sample 1

value: h- ade6-M210 leu1-32 ura4-UTRD::kanMX shura4-5/natR


title: ura4-UTRD+hp clr4∆

description: Sample 2

value: h- ade6-M210 leu1-32 ura4-UTRD::kanMX shura4-5/natR clr4∆::hphMX


title: WT+Rdp1OE

description: barcode: TTAGGC


title: WT+Ago1OE

description: barcode: ATCACG


title: rdp1∆

data_processing:
Reads with minimum 20 nt length and maximum 1 mismatch were aligned using the basic pipeline of the Helisphere software. Reads mapping to more than one location were randomly assigned.
Files were normalized for reads per million and converted to IGV-viewable formats.
Genome_build: S. pombe h- (GCA_000002945.1)
Supplementary_files_format_and_content: IGV-viewable files are tab delimited and include reads per million at each nucleotide position.

source_name: rdp1∆_haploid cells

growth_protocol: Cells were grown in YES

extract_protocol:
RNA was extracted using the hot phenol method (Leeds et al., 1991) and further purified using the RNeasy kit from Qiagen according to manufacturer's protocols.
No library construction- total purified RNA was run on flowcells containing dT oligos (Ozsolak et al., 2010: "Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation")

value: h- ade6-M210 leu1-32 rdp1∆::hphMX


title: WT

source_name: WT_haploid cells


title: WT+vector IP

description: barcode: ATCACG

value: PDM 829


title: WT+Dcr1OE

description: barcode: CAGATC

value: H3K9me2A (bcam, ab1220)


title: ura4+hp

description: Sample 4

value: h- ade6-M210 leu1-32 shura4-5/natR


title: ura4-UTRD+hp rdp1∆

description: Sample 7

value: h- ade6-M210 leu1-32 ura4-UTRD::kanMX shura4-5/natR rdp1∆::hphMX


title: ura4-UTRDIS+hp

description: Sample 5

value: h- ade6-M210 leu1-32 ura4-UTRDIS/kanMX shura4-5/natR


title: WT+vector input

description: barcode: GGCTAC

value: none, input DNA


title: ec-jl-794-orthoE

status: Public on Dec 25 2013

city: Berkeley

first: Lior

last: Pachter

address: 1081 Evans Hall, Department of Mathematics, University of California at Berkeley

department: Mathematics and Molecular and Cell Biology

institute: UC Berkeley

data_processing:
Read alignments using bowtie 0.12.7and Ensembl 67
bowtie -aS -X 700 --chunkmbs 128 --maqerr 100 --offrate 1 -v 3
Isoform quantification using eXpress version 1.2.0
express -B 2
Genome_build: hg19
Supplementary_files_format_and_content: Isoform quantification in a tab-delimited file including model parameters

molecule: polyA RNA

source_name: erythroblasts

growth_protocol: Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted as described (Hu, J., Liu, J., Xue, F., Halverson, G., Reid, M., Guo, A., Chen, L., Raza, A., Galili, N., Jaffray, J. et al. (2013) Isolation and functional characterization of human erythroblasts at distinct stages: implications for understanding of normal and disordered erythropoiesis in vivo. Blood, 121, 3246-3253.)

extract_protocol:
RNA was extracted from 1x 106 sorted human erythroblasts using RNeasy Plus Mini kits (Qiagen)
Illumina TruSeq

tag: differentiation stage

value: orthochromatophilic erythroblasts


title: ec-jl-794-e-basoE

value: early basophilic erythroblasts


title: ec-jl-774-polyE

value: polychromatophilic erythroblasts


title: ec-jl-794-l-basoE

value: late basophilic erythroblasts


title: ec-jl-774-orthoE


title: ec-jl-794-polyE


title: ec-jl-774-l-basoE


title: ec-jl-774-e-basoE


title: ura4-UTRD dcr1∆

description: Sample 6

value: h- ade6-M210 leu1-32 ura4-UTRD::kanMX dcr1∆::hphMX

tag: strain


title: ec-jl-774-proE

value: proerythroblasts


title: ec-jl-610-orthoE


title: ec-jl-794-proE


title: ec-jl-610-l-basoE


title: ec-jl-610-polyE


title: FibroblastVitro

city: Cambridge

first: Silvi

last: Rouskin

address: 455 Main Street

institute: Whitehead Institute

data_processing:
For human cells, stripped files were aligned to transcript model representing the longest splicing isoform, downloaded from RefSeq. For yeast cells, data was aligned to the yeast genome.
only uniquely aligned reads with less than two mismatches were taken.
Total counts per position per transcript were written to .txt files(human cells) or mapped to the yeast chromosomes in wig format
Genome_build: hg19(human cells) or yeast genome downloaded from yeastgenome.org on October11, 2009, corresponds to assembly R62 (UCSC: sacCer2)
Supplementary_files_format_and_content: txt files (human cells) and wig files (yeast cells). The processed data are .txt files and represents alignments to the transcriptome downloaded from RefSeq. For genes with multiple splicing isoforms, the longest isoform was used. Reads were filtered for 2 or less mismatches and unique alignments only. The txt file has three colums, 1= ref seq ID, 2=position , 3= number of aligned reads that passed filters

source_name: Human fibroblasts

growth_protocol: cells were grown to 1million/ml(fibroblast) or OD=0.7 (yeast)

extract_protocol:
Total RNA was extracted with Triazol
RNA was randomply fragmented using Ambion fragmentation reagents. Fragments of 60-70mers were ligated to linker-1(IDTdna). Premature reverse transciptase producs were isolated by size selection. The cDNA was circularized with CircLigase(epicentre), and subjected to PCR for 8-10 cycles with primers for standard illumina sequencing.

treatment_protocol: 300ul or 400 ul of DMS was added to 15mls of cells

tag: cell type

value: Human fibroblasts


title: ec-jl-610-proE


title: ec-jl-610-e-basoE


title: FibroblastVivo


title: K562vivo2_dms400

data_processing:
stripped files were aligned to transcript model representing the longest splicing isoform, downloaded from RefSeq
only uniquely aligned reads with less than two mismatches were taken.
Total counts per position per transcript were written to .txt files
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are .txt files and represents alignments to the transcriptome downloaded from RefSeq. For genes with multiple splicing isoforms, the longest isoform was used. Reads were filtered for 2 or less mismatches and unique alignments only. The txt file has three colums, 1= ref seq ID, 2=position , 3= number of aligned reads that passed filters

source_name: Human bone marrow, chronic myelogenous leukemia

growth_protocol: cells were grown to 1million/ml

value: Human erythromyeloblastoid leukemia cells

tag: treated with

value: 400ul of DMS to 15mls of cells


title: K562denatured


title: DP_input

city: basel

first: maria alessandra

last: vigano

department: department of biomedicine

country: Switzerland

institute: university of basel

data_processing:
Sequence reads were mapped using Botwie version 0.12.7 with up to 2 mismatches and up to 100 best alignment positions were reported (bowtie options –v 2 –a --best --strata –m 100).
In case a read had more hits n to an individual sequence from any of these data bases, the weight 1/n was used instead. These weights were used in all the subsequent analyses. DNA fragment length was estimated from cross correlation. profile of read density on both chromosomal strands.
Mapped reads were shifted towards their 3’ end by the half of the fragment length
Genome_build: mm9
Supplementary_files_format_and_content: WIG files were generated with a custom Perl script

source_name: DPdouble positive thymocytes derived from  in vitro expanded bone marrow cells transduced with Nup98-HoxB4, grown with IL7 and DLL4 (Notch signaling) and injected into Rag2-/- mouse

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Libraries were prepared according to Illumina's instructions accompanying the Agilent_DNA _Kit _100.  The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were generated and sequenced on the Genome Analyzer following the Illumina manufacturer's protocols.

tag: chip antibody


title: FibroblastDenatured


title: R15

city: Chapel Hill

first: Zefeng

last: Wang

state: NC

address: 4113 Genetic Medicine

department: Pharmacology

institute: UNC

description: Sample 1

data_processing:
Sequenced reads were mapped to hg19 whole genome using MapSplice v2.1.2 with default parameters
FPKM (fragments per kilobase of exon per million fragments mapped) were calculated using Cufflinks
The changes of splicing isoforms were analyzed by MISO pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values are included in the cufflink output files for each sample

source_name: HEK 293T_control

growth_protocol: Cells were grown on DMEM complete medium (GIBCO, BRL) supplemented with 10%FBS and without antibiotics upto 80% confluency at standard cell culture conditions.

extract_protocol:
The cells dislodged form plates using PBS  and total RNA was purified using Qiagen RnaEasy Minikit
The polyadenylated RNA were purified to construct sequencing library using Illumina TruSeq Total RNA Sample Prep kits (conducted by UNC High Throughput Sequencing Facility)

treatment_protocol: The samples described are stable lines expressing shRNA DAZAP1 (plKO.1) or control shRNA and are selected on puromycin

value: HEK 293T

value: expressing control shRNA; wild type


title: R16

description: Sample 2

source_name: HEK 293T_DAZAP1 knockdown

value: expressing shRNA DAZAP1 (plKO.1); DAZAP1 knockdown


title: ProT_input

source_name: ProT in vitro expanded bone marrow cells transduced with Nup98-HoxB4 and grown with IL7 and DLL4 (Notch signaling)


title: DP_H3K4me3_rep1

value: double positive thymocytes derived from  in vitro expanded bone marrow cells transduced with Nup98-HoxB4, grown with IL7 and DLL4 (Notch signaling) and injected into Rag2-/- mouse

value: anti H3K4me3 antibody (Abcam ab8580)

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: Abcam


title: DP_H3K4me3_rep2


title: DP_H3K27me3_rep1

value: anti H3K27me3 antibody (Cell Signaling #9733)

value: Cell Signaling


title: ProT_H3K4me3_rep2

value: in vitro expanded bone marrow cells transduced with Nup98-HoxB4 and grown with IL7 and DLL4 (Notch signaling)


title: ProT_H3K27me3_rep2


title: HSC_input

source_name: HSC in vitro expanded bone marrow cells transduced with Nup98-HoxB4


title: ProT_H3K27me3_rep1


title: ProT_H3K4me3_rep1


title: HSC_H3K4me3_rep2

value: in vitro expanded bone marrow cells transduced with Nup98-HoxB4


title: HSC_H3K27me3_rep1


title: HSC_H3K27me3_rep2


title: HSC_H3K4me3_rep1


title: k562vitro


title: Yeast10CDMS

organism: Saccharomyces cerevisiae


title: K562vivo1_dms300

value: 300ul of DMS to 15mls of cells


title: YeastNoATPDMS


title: SW480_CDK8_ChipSeq

status: Public on Dec 24 2013

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against SW480_CDK8
barcode: GTTTCG

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For samples Colo741_WCE_ChipSeq, Colo741_H3K27ac_ChipSeq, HT29_CDK8_ChipSeq, HT29_WCE_ChipSeq, HT29_H3K27ac_ChipSeq, SW480_WCE_ChipSeq, and SW480_CDK8_ChipSeq reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Colon Carcinoma

growth_protocol: Cells grown in Glutamax RPMI1640+10%FBS

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Nothing

tag: antibody catalog number

value: Santa Cruz SC-1521

value: Colon Carcinoma


title: DP_H3K27me3_rep2


title: HT29_H3K27ac_ChipSeq

description:
Chromatin IP against HT29_H3K27ac
barcode: TTAGGC

growth_protocol: McCoy's 5a Medium, 10% FBS

value: Abcam AB4729


title: ES_CTCF_Bis_rep1

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

description: bisulfite converted after ChIP

data_processing:
All C nucleotides in sequence reads from bisulfite converted samples were converted in silico to T nucleotides, and the converted reads were aligned to a similarly converted genome separately to each strand using the software bowtie (version 0.10.0.1)(Langmead et al., Genome Biol. 2009;10(3):212) with parameters --best --strata -v 3 --norc -a.
Only reads with a unique alignment in this reduced alphabet base-space were retained, and C nucleotides from the original reads and genome were reintroduced.
To eliminate effects caused by polymorphisms in our experimental system, C nucleotides that overlapped known SNPs between the reference C57BL/6J and the 129S5 strains were removed from further analysis based on the SNPs identified by the Mouse Genomes Project at Sanger Institute (downloaded from ftp://ftp-mouse.sanger.ac.uk/REL-1003/SNPs/20100301-all-snps.tab.gz).
Total and methylated counts for all covered CpGs in the genome were calculated as the number of alignments with either C (methylated) or T (unmethylated) and the number of alignments with C (methylated), combining the counts from the two Cs in a CpG and its reverse complement (position i on plus strand and position i+1 on minus strand).
Genome_build: mm9
Supplementary_files_format_and_content: Chromosome, Chromosomal position, Total number of reads, Number of methylated reads.

source_name: embryonic stem cells

growth_protocol: Wild type embryonic stem cells derived from mixed 129-C57Bl/6 background blastocysts, were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol. Differentiation was performed as previously described (Bibel et al).

extract_protocol: Chromatin immunoprecipitation (ChIP) assay for CTCF was performed according to the Upstate protocol using the antibody anti-CTCF (SantaCruz #15914) and starting from 70 μg of chromatin. Enrichments were checked by real time PCR using SYBR Green chemistry (ABI) and 1/80 of ChIP or 20ng of input chromatin per PCR reaction. DNA generated from 5 different ChIP experiments (≈100 ng) was pooled and used for subsequent library preparation. DNA fragments were end repaired by incubation at 20°C for 30 minutes with 400µM dNTP, 3 units of T4 DNA polymerase (NEB #M0203S), 5 units of DNA Polymerase I Lg. Frag. (Klenow) (NEB #M0210S), 10 units of T4 PNK (NEB #M0201S), 1x T4 DNA ligase buffer containing 10mM ATP (NEB), followed by column purification using QIAquick PCR Purification Kit (QIAGEN #28106). 3’ ends of DNA fragments were adenylated by incubation at 37°C for 30 minutes with 200µM dATP, 1xNEB Buffer 2, 5 units Klenow Fragment (3´->5´ exo–) (NEB # M0212L), followed by column purification using MinElute PCR Purification Kit (QIAGEN # 28006). Adapter for single end sequencing were reproduced based on Illumina adapter sequences (Oligonucleotide sequences © 2006-2008 Illumina, Inc. All rights reserved): 5’ P- GATXGGAAGAGXTXGTATGXXGTXTTXTGXTTG and 5’ AXAXTXTTTXXXTAXAXGAXGXTXTTXXGATXT, where X is a methylated cytosine. Adapters were ordered as single stranded oligos (Microsynth AG), resuspended in annealing buffer (10mM Tris pH7.5, 50mM NaCl, 1mM EDTA), annealed by heating at 95°C for 10 minutes and cooling down slowly. Annealed adapters were ligated to the DNA fragments by incubation at room temperature for 15 minutes in the following mix: 400 nM of annealed adapters, 1x NEB Quick ligase buffer, 2.000 units of T4 Quick ligase (NEB #M2200S), followed by column purification using MinElute PCR Purification Kit (QIAGEN #28006). 200 ng of Drosophila DNA (Kc cells) were then added as a carrier. Adapter-ligated DNA of 150-400 bp was selected from 2% agarose gel electrophoresis and purified using MinElute Gel Extraction Kit (QIAGEN #28606). BSA (final concentration 0.5μg/μl) was added to gel-purified DNA and the mix was then treated with sodium bisulfite using the Imprint® DNA Modification Kit (Sigma-Aldrich) as per manufacturer’s instructions. Bisulfite-converted, adapter-ligated DNA molecules were enriched using 18 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 μl 10X PfuTurbo reaction buffer, 25 μM dNTPs, 0.5µM of Single End Illumina PCR primers (1.1 and 2.1). The thermocycling parameters were: 95°C 2 min, 98°C 30 sec, then 18 cycles of 98°C 15 sec, 65°C 30 sec and 72°C 3 min, ending with one 72°C 5 min step, and 4°C indefinitely, followed by column purification using the MinElute PCR Purification Kit (QIAGEN #28006). DNA was then run on 2% agarose gel electrophoresis to separate the library from adapter-adapter ligation products, and purified from the gel using the MinElute Gel Purification Kit (QIAGEN #28606). Quality of the libraries and template size distribution were assessed by running an aliquot of the library on an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: embryonic stem cells

tag: genotype/variation

value: wild type

value: anti-CTCF (SantaCruz #15914)


title: SW480_WCE_ChipSeq

description:
Chromatin IP against SW480_WCE
barcode: GTGAAA

value: None WCE


title: NP_hMeDIPseq_rep1

description: MeDIP against 5-hmC

data_processing:
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses.
Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads).
Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using custom perl script, score represents read count in 100bp window

source_name: neuronal progenitor cells

growth_protocol: Wild-type embryonic stem cells (129-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))

extract_protocol: Genomic DNA was isolated from cell pellets and subsequently fragmented to 200-1000 bp fragments with a Bioruptor (Diagenode, Sparta, NJ). The protocol for the library preparation was adapted from Illumina Genomic DNA Sample Preparation Guide. Briefly, 7 to 10 ug of fragmented DNA were end repaired. 3’ ends of DNA fragments were adenylated. Genomic single end or paired end adapters were annealed.  hMeDIP was performed as previously described (Ref. Weber). Briefly, 4ug of adapter-ligated DNA were denatured and immunoprecipitated with 4ul of a 1:10 dilution of rabbit polyclonal anti-hmC antibody (Active Motif #39770) for 2 hours, before 40 ul of Protein A Dynabeads (Invitrogen, #100.02D) were added for another 2 hours. Bound DNA was isolated from the beads by 3 hours digestion with Proteinase K, extracted by phenol-chlorophorm and amplified by 18 cycles of PCR following the conditions in the Illumina Genomic DNA Sample Preparation Guide and followed by column purification using the MinElute PCR purification kit (QIAGEN #28006). Fragments of 250-300 bp (for single end sequencing) or 400-450 (for paired end sequencing) were size-selected from 2% agarose gel and purified using the MinElute Gel Purification Kit (QIAGEN #28606) Quality of the libraries and template size distribution were assessed by running an aliquot of the library on an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: ES-derived neuronal progenitor cells

value: anti-5hmC (Active Motif #39770)


title: ES_hMeDIPseq_rep1

description: MeDIP against 5-hmC


title: HT29_WCE_ChipSeq

description:
Chromatin IP against HT29_WCE
barcode: GCCAAT


title: Colo741_H3K27ac_ChipSeq

description:
Chromatin IP against Colo741_H3K27ac
barcode: GATCAG


title: Colo741_WCE_ChipSeq

description:
Chromatin IP against Colo741_WCE
barcode: CTTGTA


title: LY1_JQ1_POL2_ChipSeq

description:
Chromatin IP against LY1_JQ1_POL2
barcode: GGCTAC

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For samples Colo741_WCE_ChipSeq, Colo741_H3K27ac_ChipSeq, HT29_CDK8_ChipSeq, HT29_WCE_ChipSeq, HT29_H3K27ac_ChipSeq, SW480_WCE_ChipSeq, and SW480_CDK8_ChipSeq reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
For samples LY1_WT_WCE_ChipSeq, LY1_JQ1_WCE_ChipSeq, LY1_DMSO_WCE_ChipSeq, LY1_DMSO_BRD4_ChipSeq, LY1_DMSO_POL2_ChipSeq, LY1_JQ1_BRD4_ChipSeq, LY1_WT_MED1_ChipSeq, and LY1_JQ1_POL2_ChipSeq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Diffuse Large B-Cell Lymphoma

growth_protocol: RPMI 1640 supplemented with 20% FCS and 1% GlutaMAX.

treatment_protocol: 500nM JQ1 for 6 hours

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899

value: Diffuse Large B-Cell Lymphoma


title: LY1_WT_MED1_ChipSeq

description:
Chromatin IP against LY1_WT_MED1
barcode: CTTGTA

value: Bethyl A300-793A


title: LY1_DMSO_BRD4_ChipSeq

description:
Chromatin IP against LY1_DMSO_BRD4
barcode: ACTTGA

treatment_protocol: 0.05% DMSO for 6 hours

value: Bethyl A301-985A


title: LY1_JQ1_WCE_ChipSeq

description:
Chromatin IP against LY1_JQ1_WCE
barcode: TGACCA


title: LY1_JQ1_BRD4_ChipSeq

description:
Chromatin IP against LY1_JQ1_BRD4
barcode: TAGCTT


title: LY1_WT_WCE_ChipSeq

description:
Chromatin IP against LY1_WT_WCE
barcode: ACAGTG


title: Ribodepleted 8h

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

description: Sample 11

data_processing:
Illumina 1.9 basecalling
Alignment to the Akata EBV genome (NCBI accession number KC207813.1) using Bowtie version 2 with parameters --library-type fr-firststrand, default options
Generation of signalmap files using IGVTools
Genome_build: KC207813.1
Supplementary_files_format_and_content: Signalmap coverage files for the Akata genome

source_name: Akata_Ribodepleted 8h

growth_protocol: Cells were grown at 37°C and 5% CO2 in a humidified incubator and were cultured in RPMI 1640 plus 10% fetal bovine serum and 0.5% Penicillin-Streptomycin.

extract_protocol:
RNeasy minikit (Qiagen) or Trizol reagent (Ambion)
Illumina TruSeq Stranded protocol

treatment_protocol: One day prior to induction, near-saturation cell cultures were diluted with equal volumes of fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep). The next day, cells were spun down and resuspended at a concentration of 1 x 10^6 cells/ml in fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep) plus either 10 μg/ml anti-IgG or no anti-IgG (uninduced).

value: Akata

value: An Epstein-Barr virus (EBV)-producer line

tag: time after induction

value: 8 hours

value: Ribo-Zero treated RNA


title: Ribodepleted 48h

description: Sample 13

source_name: Akata_Ribodepleted 48h

value: 48 hours


title: Ribodepleted 4h

description: Sample 10

source_name: Akata_Ribodepleted 4h

value: 4 hours


title: Ribodepleted 30m

description: Sample 7

source_name: Akata_Ribodepleted 30m

value: 30 minues


title: Ribodepleted 5m

description: Sample 6

source_name: Akata_Ribodepleted 5m

value: 5 minutes


title: Ribodepleted 0

description: Sample 5

source_name: Akata_Ribodepleted 0

value: 0 (uninduced)


title: Ribodepleted induced

description: Sample 4

source_name: Akata_Ribodepleted induced

value: 24 hours


title: Ribodepleted uninduced

description: Sample 3

source_name: Akata_Ribodepleted uninduced


title: HT29_CDK8_ChipSeq

description:
Chromatin IP against HT29_CDK8
barcode: ACAGTG

value: Santa Cruz SC-1521

value: Colon Carcinoma


title: Poly(A)-selected induced

description: Sample 2

source_name: Akata_Poly(A)-selected induced

value: poly(A) RNA


title: Poly(A)-selected uninduced

description: Sample 1

source_name: Akata_Poly(A)-selected uninduced


title: 3m_DKO_H3K27me3_ChIP-seq

city: Cheonan

first: Keunsoo

last: Kang

institute: Dankook University

data_processing:
Basecalls were performed using the CASAVA software.
RNA-seq: Sequenced reads were aligned to the mm9 genome assembly using TopHat (Trapnell et al., Bioinformatics, 2009). Transcript abundance was estimated by means of fragment per kilobase of exon per million fragments mapped (FPKM) using Cufflinks (Trapnell et al., Nat. Protocol, 2012).
ChIP-seq: Sequenced reads were aligned to the mm9 genome assembly using BWA (Li and Durbin, Bioinformatics, 2009). H3K27me3 and H3K4me3 peaks were identified using SICER (Zang et al., Bioinformatics, 2009) and HOMER (Heinz et al., Mol Cell, 2010), respectively.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BedGraph files (ChIP-seq) and tab-delimited text file containing FPKM values (RNA-seq).

source_name: Liver tissue, DKO, 3 months, H3K27me3 ChIP

growth_protocol:
Animals were handled and housed in accordance with the guidelines of NIH and all experiments were approved by the Animal Care and Use Committee of NIDDK.
2-month, 8-month and 3-month (injected with CCL4) old mice in Ezh2fl/fl (WT), Ezh1-/- (E1KO), Ezh2fl/flAlb-Cre (E2KO) and Ezh1-/-Ezh2fl/flAlb-Cre (DKO) were used for RNA-seq. 3-month-old mice were used for ChIP-seq.

extract_protocol:
ChIP-sequencing was initially performed and processed by Active Motif, Inc. (Carlsbad, CA) on mouse liver tissues.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: tissue

value: liver

tag: age

value: 3 months

value: H3K27me3 (in-house antibody by Active Motif, Carlsbad, CA)


title: 3m_E1KO_H3K27me3_ChIP-seq

source_name: Liver tissue, E1KO, 3 months, H3K27me3 ChIP


title: 3m_Input_Control_ChIP-seq

source_name: Liver tissue, pooled, 3 months, input

value: pooled


title: 6T1

city: Singapore

first: Weiling

last: Zheng

address: Science Drive 4

country: Singapore

institute: National University of Singapore

description:
Sample 3
SAGE sequencing

data_processing:
The SOLiD-generated RNA-Seq reads was in 27 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches.
The expression levels of mapped transcripts were normalized into transcript per million (TPM) to faciliate comparison among different samples.
Genome_build: danRer7
Supplementary_files_format_and_content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.

organism: Danio rerio

source_name: liver tumor

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, USA) and treated with DNase I to remove genomic DNA contamination.
Library construction was conducted by Mission Biotech (Taiwan) following standard ABI SOLiD protocol.

treatment_protocol: one-month-old transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.

value: Tg(fabp10:LexPR-LexA:EGFP; cryB:mCherry-NLS-Cre; fabp10:loxP-mCherry-loxP-EGFP-krasV12) line

tag: agent

value: mifepristone

tag: outcome

value: liver tumorigenesis


title: LY1_DMSO_POL2_ChipSeq

description:
Chromatin IP against LY1_DMSO_POL2
barcode: GATCAG

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899

tag: cell line

value: Diffuse Large B-Cell Lymphoma


title: 3m_E2KO_H3K27me3_ChIP-seq

source_name: Liver tissue, E2KO, 3 months, H3K27me3 ChIP


title: 3m_E1KO_H3K4me3_ChIP-seq

source_name: Liver tissue, E1KO, 3 months, H3K4me3 ChIP

value: H3K4me3 (in-house antibody by Active Motif, Carlsbad, CA)


title: 6T2

description:
Sample 4
SAGE sequencing


title: 3m_E2KO_H3K4me3_ChIP-seq

source_name: Liver tissue, E2KO, 3 months, H3K4me3 ChIP


title: LY1_DMSO_WCE_ChipSeq

description:
Chromatin IP against LY1_DMSO_WCE
barcode: TTAGGC

source_name: Diffuse Large B-Cell Lymphoma

value: None WCE


title: 3m_DKO_H3K4me3_ChIP-seq

source_name: Liver tissue, DKO, 3 months, H3K4me3 ChIP


title: Ribodepleted 24h

description: Sample 12

source_name: Akata_Ribodepleted 24h

value: Akata

value: An Epstein-Barr virus (EBV)-producer line

tag: molecule subtype

value: Ribo-Zero treated RNA


title: 3m_WT_H3K4me3_ChIP-seq

source_name: Liver tissue, WT, 3 months, H3K4me3 ChIP

value: Ezh2fl/fl (wild type)


title: Ribodepleted 2h

description: Sample 9

source_name: Akata_Ribodepleted 2h

value: 2 hours


title: Ribodepleted 1h

description: Sample 8

source_name: Akata_Ribodepleted 1h

value: 1 hour


title: 6M1

description:
Sample 1
SAGE sequencing

source_name: control liver

value: liver

value: control


title: 3m_E1KO-CCL4_RNA-seq_rep1-3

description: mRNA-seq

source_name: Liver tissue, E1KO, 3 months, CCL4

extract_protocol:
RNA was purified twice from 1 ug total RNA, and cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For the CCL4 treatment, WT, E1KO, E2KO and DKO mice were injected with CCL4 at 2 ml/kg intraperitoneally twice a week for two weeks, starting at 3 months of age. After 24 h of the last treatment, all the animals were sacrificed.

value: 3 months

tag: treatment


title: 3m_WT-CCL4_RNA-seq_rep1-3

description: mRNA-seq

source_name: Liver tissue, WT, 3 months, CCL4


title: 3m_E2KO-CCL4_RNA-seq_rep1-3

description: mRNA-seq

source_name: Liver tissue, E2KO, 3 months, CCL4


title: 8m_DKO_RNA-seq_rep1-2

description: mRNA-seq

source_name: Liver tissue, DKO, 8 months

value: 8 months


title: 8m_E1KO_RNA-seq_rep1-2

description: mRNA-seq

source_name: Liver tissue, E1KO, 8 months


title: 8m_E2KO_RNA-seq_rep1-2

description: mRNA-seq

source_name: Liver tissue, E2KO, 8 months


title: 8m_WT_RNA-seq_rep1-2

description: mRNA-seq

source_name: Liver tissue, WT, 8 months


title: 3m_WT_H3K27me3_ChIP-seq

source_name: Liver tissue, WT, 3 months, H3K27me3 ChIP

value: H3K27me3 (in-house antibody by Active Motif, Carlsbad, CA)


title: 2m_E2KO_RNA-seq_rep1-3

description: mRNA-seq

source_name: Liver tissue, E2KO, 2 months

value: 2 months


title: 2m_DKO_RNA-seq_rep1-3

description: mRNA-seq

source_name: Liver tissue, DKO, 2 months


title: 2m_E1KO_RNA-seq_rep1-3

description: mRNA-seq

source_name: Liver tissue, E1KO, 2 months


title: 2m_WT_RNA-seq_rep1-3

description: mRNA-seq

source_name: Liver tissue, WT, 2 months


title: IgG ChIP-seq result

city: Ann Arbor

first: Yibin

last: Chen

state: MI

address: 1115 w medical drive

institute: university of Michigan

description: Antibody: rabbit anti-mH2ABbd (home-made)

data_processing:
The read quality of each sample was determined by FastQC software. After prefiltering the raw data by removing sequenced adapters and low quality reads, the tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Parameter settings were as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5’ and 3’ end to remove low-quality bases). Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu). Parameters settings were as follows: tag size with 25bp, band width with 300bp, P-value cutoff for peak detection was set to 1e-05. The peaks obtained from ChIP sequencing were matched to the annotated reference genome (mouse mm9) using Cisgenome 2.0
Genome_build: mm9
Supplementary_files_format_and_content: The tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Peak detection was performed using MACS software from Galaxy browser.

source_name: Mouse ES cells (C57Bl/6)

growth_protocol: All procedures are to be done under sterile conditions in a laminar flow hood using sterile instruments and detergent-free glassware. Dulbecco’s modified Eagle’s media (DMEM)  is pared for ES cell medium.

extract_protocol:
Mouse ES cells were crosslinked with formaldehyde treatment. The chromatin were isolated from 1 × 108 cells and fragmented to 200 to 400 bp by sonication. For MeDIP, we sonicated genomic DNA to produce random fragments ranging in size from 100 to 400 bp.
DNA were repaired to blunt ends by T4 DNA polymerase and phosphorylated with T4 polynucleotide kinase using the END-IT kit (Epicentre). A single “A” base was added to 3’ end with Klenow. Double-stranded adaptors were ligated to the fragments with DNA ligase. Ligation products between 200 and 600 bp were gel purified on 2% agarose to remove unligated adaptors and subjected to 20 PCR cycles. For MeDIP, The DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3’-A base used for adaptor ligation. Following ligation of a pair of adaptors to the repaired ends, the fragments around 160 bp to 370 bp isolated from agarose gel.We used 1 ug of fragmented DNA for a standard MeDIP assay as described. Following denaturation at 95°C for 10 min, immunoprecipitation was carried at 4°C for 1 hr using 1 μg of monoclonal antibody against 5-methylcytidine  in a final volume of 500 μl IP buffer (10 mM sodium phosphate (pH 7.0), 140 mM NaCl, 0.05% Triton X-100) and incubate at 4 C for 12 hours. And we added the mixture with 40 μl of Protein A/G beads (20421, Pierce) and Rabbit anti-mouse IgG (315-005-008, Jackson Immunoresearch) for 2 hr at 4°C and washed it for times with 700 μl of IP buffer. We then treated the beads with proteinase K for 2 hr at 50°C and recovered the methylated DNA by phenol-chloroform extraction followed by ethanol precipitation. Then the MeDIP-enriched DNA was amplified using the adaptor primers for 15 cycles and the fragments around 220 bp to 420 bp were isolated from agarose gel.

treatment_protocol: Mouse ES cells were cultured in LIF alone without a feeder layer before harvest.

tag: barcode

value: CTTGTA

tag: strain

tag: antibody

value: Rabbit IgG


title: 5mC MeDIP-seq-3 result

description: Antibody: mouse anti-5-Methylcytosine (Clone 33D3)

value: TAGCTT


title: IgG MeDIP-seq result

value: CGATGT

value: Mouse IgG


title: 3m_DKO-CCL4_RNA-seq-rep1-3

description: mRNA-seq

source_name: Liver tissue, DKO, 3 months, CCL4


title: MeDIP-seq-2 result

data_processing:
The read quality of each sample was determined by FastQC software. After prefiltering the raw data by removing sequenced adapters and low quality reads, the tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Parameter settings were as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5’ and 3’ end to remove low-quality bases). Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu). Parameters settings were as follows: tag size with 25bp, band width with 300bp, P-value cutoff for peak detection was set to 1e-05. The peaks obtained from ChIP sequencing were matched to the annotated reference genome (mouse mm9) using Cisgenome 2.0
Genome_build: mm9
Supplementary_files_format_and_content: The tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Peak detection was performed using MACS software from Galaxy browser.
Genome Build:
5mC_2.bed: mm9

value: GCCAAT

value: mouse anti-5-Methylcytosine (Clone 33D3)

tag: cell type

value: ES cells


title: 6M2

description:
Sample 2
SAGE sequencing

value: Tg(fabp10:LexPR-LexA:EGFP; cryB:mCherry-NLS-Cre; fabp10:loxP-mCherry-loxP-EGFP-krasV12) line


title: ES_MeDIPseq_rep1

description: MeDIP against 5-mC

data_processing:
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses.
Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads).
Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: wig files were generated using custom perl script, score represents read count in 100bp window

source_name: embryonic stem cells

extract_protocol: Genomic DNA was fragmented to 200-1000bp fragments with a Bioruptor (Diagenode, Sparta, NJ). The protocol for the library preparation was adapted from Illumina Genomic DNA Sample Preparation Guide. Briefly, 7 to 10µg of fragmented DNA were end repaired and their 3’ ends adenylated. Genomic single end or paired end adapters were annealed. MeDIP was performed using 4ug of adapter-ligated DNA and 10 µl of mouse monoclonal 5mC antibody (Eurogentec #BI-MECY-1000) for 2 hrs, followed by addition of , before 40µl of Protein A Dynabeads (Invitrogen, #100.02D, hMeDIP) or Dynabeads M-280 Sheep anti-mouse IgG (Dynal Biotech #112.01) were added for another 2 hrs. Immunoprecipitated DNA was amplified by 18 cycles of PCR following the Illumina Genomic DNA Sample Preparation Guide and purified using the MinElute PCR purification kit. Fragments of 250-300bp (for single end sequencing) or 400-450bp (for paired end sequencing) were size-selected from 2% agarose gel and purified using the MinElute Gel Extraction Kit. Quality of the libraries and template size distribution were checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Embryonic Stem Cells (ES)

tag: genotype

value: wild type

tag: chip antibody

value: anti 5mC antibody (Eurogentec #BI-MECY-1000)


title: ES_CTCF_Bis_rep2

description: bisulfite converted

value: anti-CTCF (SantaCruz #15914)


title: NP_MeDIPseq_rep1

description: MeDIP against 5-mC

source_name: neuronal progenitor cells

value: ES-derived neuronal progenitor cells


title: H2A.B ChIP-seq result

data_processing:
The read quality of each sample was determined by FastQC software. After prefiltering the raw data by removing sequenced adapters and low quality reads, the tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Parameter settings were as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5’ and 3’ end to remove low-quality bases). Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu). Parameters settings were as follows: tag size with 25bp, band width with 300bp, P-value cutoff for peak detection was set to 1e-05. The peaks obtained from ChIP sequencing were matched to the annotated reference genome (mouse mm9) using Cisgenome 2.0
Genome_build: mm9
Supplementary_files_format_and_content: The tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Peak detection was performed using MACS software from Galaxy browser.
Genome Build:
H2A.B.bed: MM9

value: CAGATC

value: rabbit anti-mH2ABbd (home-made)


title: NP_hMeDIPseq_rep2

description: MeDIP against 5-hmC

value: anti-5hmC (Active Motif #39770)


title: ES_MeDIPseq_rep2

description: MeDIP against 5-mC


title: RESTko_ES_Bis

description: bisulfite converted

source_name: REST knockout ES cells

growth_protocol: REST KO embryonic stem cells derived from Black Agouti 129 background blastocysts, were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol. Differentiation was performed as previously described (Bibel et al).

extract_protocol: The REST KO methylome library was prepared following Illumina Paired-End Sample Preparation Guide, with the following modifications: Upon adapter ligation and gel selection, purified DNA was converted with sodium bisulfite using the Imprint DNA Modification Kit (Sigma-Aldrich) as per manufacturer's instructions. One third of the bisulfite-converted, adapter-ligated DNA molecules were enriched by PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5ul 10X PfuTurbo reaction buffer, 25uM dNTPs, 0.5uM of Illumina PE-PCR primers. The thermocycling parameters were: 95C 2 min, 98C 30 sec, then 10 cycles of 98C 15 sec, 65C 30 sec and 72C 3 min, ending with one 72C 5 min step. Amplified DNA was then purified using Agencourt AMPure XP beads (Beckman-Coulter). Quality of the libraries and template size distribution were assessed by running an aliquot of the library on an Agilent 2100 Bioanalyzer (Agilen Technologies).

value: Black Agouti 129

value: REST knockout


title: DNase-Seq (DNSnf2h) 2

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description: DNase-Seq (-Tet, dominant-negative Snf2h)

data_processing:
Illumina Casava 1.6 software was used for basecalling.
Areas of enrichment were identified using DNase2Hotspots software(https://sourceforge.net/projects/dnase2hotspots) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9
Supplementary_files_format_and_content: comma-delimited (CSV)  text files include genomic locations (Chromosome, start,  end ), z-score, p-value and the maximum density of hotspots.

source_name: 3134-tet (DNSnf2h)

growth_protocol: The 3134 murine mammary epithelial cell line, originally derived from a subclone of 904.13, was maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS, Atlanta Biologicals, Lawrenceville, GA), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 2 mM L-glutamine, and 5 mg/ml penicillin-streptomycin in a 37°C incubator with 5% C02.

extract_protocol: Expression of dominant-negative variant proteins was induced by removal of tetracycline for 48 hrs prior to harvest by trypsinization. Nuclei from harvested cells were isolated and digested with 60-80 U/ml DNase I (Roche, Indianapolis, IN) for 3 min at 37°C. Digested DNA were incubated at 55°C with 10 μg/ml RNase A (Roche) for a few hours to overnight followed by addition of 25 μg/ml Proteinase K (Ambion, Austin, TX) and incubation at 55°C for at least 4 hrs. DNA fragments were purified by phenol/chloroform extraction and ultracentrifugation through a sucrose gradient. After purification, fragments (between 100 and 500 bp in size) were then pooled, precipitated and assembled into libraries for sequencing.

treatment_protocol: To generate dominant-negative variant cell lines, the coding sequence of human SNF2H (hSNF2H) fused to the FLAG tag sequence at the N-terminus in the pCI-neo vector was received as a gift from David Picketts (U. of Ottawa). Using BamHI and SalI restriction enzyme sites, FLAG-hSNF2H was cloned into a tetracycline-inducible retroviral vector (pRevTRELink,  followed by site-directed mutagenesis of lysine 211 to arginine using the QuikChange XL Site Directed Mutagenesis Kit according to the manufacturer’s instructions (Stratagene, La Jolla, CA). This dominant-negative variant of FLAG-hSNF2H (dnSnf2h) was then stably integrated into a cell line containing the tetracycline transactivator regulatory system (3134Tet, 7110).  Similarly, the coding sequence of mouse Chd4 (a gift from John Svaren (U. of Wisconsin)) was cloned into pRevTRELink containing a triple FLAG tag sequence using NotI/SalI restriction enzyme sites followed by site-directed mutagenesis of lysine 250 to cysteine and integration into the 3134Tet cell line. . Constructs were fully sequenced to confirm accuracy prior to cell line integrations. All tetracycline-regulated cell lines were maintained in DMEM and 5 μg/ml tetracycline to repress expression of the dominant-negative proteins. For experiments, cells were plated in DMEM supplemented with 10% charcoal-dextran treated FBS with or without tetracycline for 48 hrs.


title: DNase-Seq (DNSnf2h) 1

description: DNase-Seq (+Tet, dominant-negative Snf2h)

source_name: 3134+tet (DNSnf2h)

value: 3134 murine mammary epithelial cell line


title: DNase-Seq (DNBrg1) 2

description: DNase-Seq (-Tet, dominant-negative Brg1 )

source_name: 3134-tet (DNBrg1)


title: DNase-Seq (DNBrg1) 1

description: DNase-Seq (+Tet, dominant-negative Brg1 )

source_name: 3134+tet (DNBrg1)


title: DNase-Seq (-tet) 2

description: DNase-Seq (-Tet)

value: DNase-Seq (-Tet)


title: ES_hMeDIPseq_rep2

description: MeDIP against 5-hmC

value: embryonic stem cells


title: DNase-Seq (DNCHD4) 1

description: DNase-Seq (+Tet, dominant-negative CHD4 )

source_name: 3134+tet (DNCHD4)


title: DNase-Seq (+tet) 1

description: DNase-Seq (+Tet)

value: DNase-Seq (+Tet)


title: DNA input 2

description: DNA input

data_processing:
Illumina Casava 1.6 software was used for basecalling.
Areas of enrichment were identified using DNase2Hotspots software(https://sourceforge.net/projects/dnase2hotspots) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: comma-delimited (CSV)  text files include genomic locations (Chromosome, start,  end ), z-score, p-value and the maximum density of hotspots.

source_name: 3134 cells

value: untreated

tag: replicate

value: replicate 2


title: DNA input 1

description: DNA input

value: replicate 1


title: Snf2h ChIP-Seq 1

description: Snf2h ChIP-Seq


title: monoclonal Brg1 ChIP-Seq 1

description: monoclonal Brg1 ChIP-Seq

value: monoclonal Brg1


title: Snf2h ChIP-Seq 2

description: Snf2h ChIP-Seq


title: silique

status: Public on Dec 23 2013

first: Huan

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Sequenced reads were mapped to Arabidopsis whole genome (TAIR10) using Tophat.
Genome_build: Arabidopsis Thaliana TAIR10

organism: Arabidopsis thaliana

source_name: WT silique

growth_protocol: Col-0 seedlings were grown on MS plates for two weeks and transferred to soil under long day conditions (16 hours light). 3 week old seedlings were bombarded with uncoated 0.6 um gold particles using a Biolistic PDS-1000/He Particle Delivery System (Bio-Rad), to simulate plasmid transformation, although no plasmid was used for these samples. Plants were grown for 18 days after bombarding. Leaves, flowers (inflorescences) and siliques were collected from these 5.5 week old plants and immediately frozen in liquid nitrogen.

extract_protocol: RNA was extracted using the Qiagen RNeasy Plant Mini kit. Extracted RNA was treated with Turbo DNase (Life Technologies AM2238) according to product specification. DNase treated RNA was then applied again to a RNeasy spin column with 0.5 volumes of ethanol, washed and eluted according to kit instructions.

tag: ecotype

value: silique


title: monoclonal Brg1 ChIP-Seq 2

description: monoclonal Brg1 ChIP-Seq


title: CHD4 ChIP-Seq 1

description: CHD4 ChIP-Seq


title: MeDIP-seq-1 result

data_processing:
The read quality of each sample was determined by FastQC software. After prefiltering the raw data by removing sequenced adapters and low quality reads, the tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Parameter settings were as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5’ and 3’ end to remove low-quality bases). Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu). Parameters settings were as follows: tag size with 25bp, band width with 300bp, P-value cutoff for peak detection was set to 1e-05. The peaks obtained from ChIP sequencing were matched to the annotated reference genome (mouse mm9) using Cisgenome 2.0
Genome_build: mm9
Supplementary_files_format_and_content: The tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Peak detection was performed using MACS software from Galaxy browser.
Genome Build:
5mc_1.bed: MM9

value: TGACCA

value: mouse anti-5-Methylcytosine (Clone 33D3)

value: ES cells


title: CHD4 ChIP-Seq 2

description: CHD4 ChIP-Seq


title: inflorescence

source_name: WT inflorescence

value: inflorescence


title: WCE_Jurkat_ChipSeq

description: WCE for Jurkat

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples, reads were aligned with bowtie 0.12.9 to the mm9 genome.  Aligned sequences were processed with MACS 1.4.2 with parameters -w -S --space=50 --keep-dup=auto -p 1e-9. Counts were normalized to reads per million.

source_name: T-ALL cell line

growth_protocol: Cells grown in RPMI1640+10%FBS

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Treated with DMSO control.

tag: antibody catalog number

value: None WCE

value: Jurkat


title: RNAPol2_Jurkat_flavopiridol_6hr_ChipSeq

description: Chromatin IP against Total RNAPol2 in Jurkat_flavopiridol_6hr

treatment_protocol: Treated with 250nM flavopiridol for 6 hours.

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899

tag: concentration

tag: drug

value: flavopiridol

tag: duration of treatment

value: 6 hr