title: K562 PRO-Seq

city: Ithaca

first: Leighton

middle: James

last: Core

address: 417 Biotechnology Building

department: Moleular Biology and Genetics

institute: Cornell University

description:
cDNA (from nascent RNA)
This Sample represents two sequencing replicates.

data_processing:
Library strategy: PRO-Seq
Pass Filter: Reads that pass filter were selected from fastq files.
Adapter Trimming: Adapter sequences were removed using Fastx tools. Reads greater than 15bp were retained.
Reverse compliment: Reads were reversed complimented using FastX tools.
rDNA filter: Reads were first mapped to a copy of rRNA gene (GenBank accession #: U13369.1) including external and internal spacers, and only reads that were not mapped to the rDNA were kept.
Mapping to the genome: Bowtie was used to map 30mers with up to two mismatches to the genome.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Processed data files are bigWigs. Each entry represents the number of reads at each base.

source_name: K562 cells

growth_protocol: K562 cells were grown to a density of 5x10^6 cells/mL in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL penicillin and 100 μg/mL streptomycin, and 2 mmol/L L-glutamine. GM12878 were cultured as described previously (GSE39878).

extract_protocol:
Nuclei isolation: All steps performed and buffers kept at 4oC. 10 mls of cells were spun down at 700g in a swinging bucket rotor for 5 min. Cells were washed in 1X cold PBS. Cells were washed in 10ml of buffer W (10mM Tris-Cl, pH 7.5, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, and 0.5 mM DTT). Cells were resuspended in 5mls of Buffer P (10mM Tris-Cl, pH 7.5, 10mM KCl, 250mM sucrose, 5mM MgCl2, 1mM EGTA, and 0.5 mM DTT, .05% tween-20 and/or .1% Igepal), and incubated 5 min. on ice. Permeabilized cells were washed twice in 5ml of buffer P, resuspended in 1ml of buffer P, and transferred to a 1.7ml eppendorf tube. Cells were pelleted at 1000 x g in a fixed angle rotor for 5min and then resuspended in 500 ml of buffer F (50 mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA, 0.5mM DTT). Cells were pelleted at 100g for 5 min, resuspended in 100 ml of buffer F, and then flash frozen in liquid nitrogen.
PRO-seq libraries were prepared as described previously (Kwak et al., 2013). Briefly, 5×10^6 nuclei were added to 2 X Nuclear Run-On (NRO) reaction mixture (10 mM Tris-HCl pH 8.0, 300 mM KCl, 1% Sarkosyl, 5 mM MgCl2, 1 mM DTT, 0.375 mM each of biotin-11-A/C/G/UTP (Perkin-Elmer), 0.8 u/µl RNase inhibitor) and incubated for 3 min at 30˚C. Nascent RNA was extracted and fragmented by base hydrolysis in 0.2 N NaOH on ice for 10~12 min, and neutralized by adding 1 X volume of 1 M Tris-HCl pH 6.8. Fragmented nascent RNA was purified using streptavidin beads, ligated with reverse 3' RNA adapter (5'p-GAUCGUCGGACUG-UAGAACUCUGAAC-/3'InvdT/), and biotin-labeled products were enriched by another round of streptavidin bead binding and extraction. For 5' end repair, the RNA products were successively treated with tobacco acid pyrophosphatase (TAP, Epicentre) and polynucleotide kinase (PNK, NEB). 5' repaired RNA was ligated to reverse 5' RNA adaptor (5'-CCUUGGCACCCGAGAAUUCCA-3') before being further purified by the third round of streptavidin bead binding and extraction. RNA was reverse transcribed using 25 pmol Illumina RP1 primer (5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA-3'). The product was amplified 15 cycles and products greater than 120 bp (insert > 70 bp) were PAGE purified before being analyzed by Illumina HiSeq 2500 instrument.

treatment_protocol: No specific treatments performed for this study.

value: chronic myelogenous leukemic cell line

tag: rna source

value: nuclear run-on

tag: pull-down strategy

value: biotin

tag: pull-down substrate

value: streptavidin


title: Pol II_noStarv

status: Public on Nov 10 2014

type: SRA

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

country: USA

institute: NIH

library_source: genomic

data_processing:
alignment, ChIP-seq: Sequence reads were obtained and mapped to the mouse mm9 genomes using the Illumina Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp (SICER).
peaks, ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958).
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph for peak files, bigWig for viewing strand specific  nuclear RNA data with the UCSC genome browser

molecule: genomic DNA

organism: Mus musculus

source_name: NIH3T3 fibroblasts

growth_protocol: NIH3T3 cells were serum-starved in the presence of 0.5% serum for 48 hr, preincubated with JQ1 (500 nM) or vehicle (DMSO) for 30 min; and stimulated with 15% serum for 30 min or left unstimulated in the continued presence of JQ1 or vehicle. Control cells and cells expressing YFP-tagged constructs were cultured in the continuous presence of 10% serum.

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

treatment_protocol:
1. NIH3T3 cells were serum-starved in the presence of 0.5% serum for 48 hr, preincubated with JQ1 (500 nM) or vehicle (DMSO) for 30 min; and stimulated with 15% serum for 30 min or left unstimulated in the continued presence of JQ1 or vehicle. Control cells were cultured in the continuous presence of 10% serum.
2. NIH3T3 cells were sequentially infected with shRNA retrovirus (pSRneo-shBRD4) and YFP or YFP-BRD4 expressing retrovirus (pMSCVpuro-YFP, pMSCVpuro-YFP-BRD4, pMSCVpuro-YFP-BRD4short or pMSCVpuro-YFP-BRD4short-mBD) in the presence of polybrene. The transduced cells were selected with G418 and puromycin.

tag: culture condition

value: continuous culture

tag: chemicals

value: DMSO

tag: chip antibody

value: Pol II (Santa Cruz Biotechnology, N20, sc-899)


title: Pol II_serum_JQ1

value: serum starved and re-fed


title: BirAmVenusUbc6_sec66∆_+CHX_2minBiotin_pulldown

city: San Francisco

first: Jonathan

last: Weissman

state: CA

address: 1700 4th Street

institute: UCSF

description: ribosome protected mRNA fragment

library_source: transcriptomic

data_processing:
Library strategy: ribosome profiling
base calls were called with Illumina CASAVA software (1.6-1.8)
3' adaptor was trimmed using a custom python script
reads were aligned sequentially first to rRNA, then unaligned reads were aligned to tRNA, then unaligned reads were aligned to a genomic index (sacCer3 for yeast) or to UCSC known gene cDNA sequences (hg19)
expression was quantitated using custom scripts after P-site mapping
Genome_build: sacCer3 and hg19
Supplementary_files_format_and_content: tab delimited file containing gene annotations, count and rpkm data

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in SD media containing 0.125 ng/ml D-biotin to OD600 .4-.6.  Mammalian cells were grown in DMEM + 10% charcoal/dextran filtered FBS biotin depleted with streptactin sepharose.

extract_protocol:
Yeast cells were harvested by filtration, flash frozen, and cryogenically pulverized in a Retsch mixer-mill.  Mammalian cells were lysed directly in plates with scraping.
Footprinting was performed with RNase I (yeast) or MNase (293 cells), monosomes purified on 10-50% sucrose gradients and biotinylated ribosomes purified on streptavidin dynabeads.  RNA was extracted with trizol and protected fragments gel purified.  Ends were repaired with T4 PNK and ligated to a pre-adenylated linker with T4 RNA Ligase 2.  Ligated fragments were gel purified, reverse transcribed and gel purified.  The cDNA was circularized then PCR amplified.

treatment_protocol: Where indicated, cells were treated with 100 µg/ml cycloheximide for 2 minutes prior to biotin induction for the times shown.  Yeast cells were induced with 10 nM biotin.  Mammalian cells were treated with 50 µM biotin

tag: genotype

value: sec66delta::KAN his3::pSEC63-BirA-mVenus-UBC6 TA-HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 leu2delta0

tag: lentivirally transduced transgenes

tag: strain


title: yeast rcm1 knockout, 90 min H2O2, polysomes

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

description: RNA polysome fraction

data_processing:
All reads were sorted by their bar codes and bar codes were subsequently removed (self-made Perl script).
Reads were aligned to the reference sequences using the Needleman-Wunsch algorithm. Before each alignment, the respective longer sequence (either the query- or the reference-sequence) was trimmed. Each sequence position was scored by following parameters: match = 10, cytosine to thymine conversion = 9, mismatch = 4, gap = 3, opening a new gap = 1
Aligned reads were filtered for sequences having less than 15% insertions or 15% deletions, or less than 20% insertions plus deletions. Sequences not fulfilling these requirements were removed (self-made Perl script).
In the remaining sequences the number of individual nucleotides was counted (self-made Perl script).
Genome_build: S. cerevisiae 25S rRNA [J01355.1] and C. elegans 28S rRNA [NR_000055.1]
Supplementary_files_format_and_content: base counts per sequence position as matrix

source_name: whole exponentially growing cells

growth_protocol: S. cerevisiae: Wild-type and rcm1 knockout yeast were grown overnight in 3 mL SC medium at 28°C with shaking. On the next day, 100 ml SD were inoculated with the overnight culture to an OD600 of 0.003 and grown at 28°C with shaking until the OD600 reached 0.5 - 0.6. C. elegans: Worms were synchronized by bleaching and cultivated until day 3 of adulthood.

extract_protocol:
RNA isolated from yeast polysome or monosome fractions was purified using Trizol (Life Technologies), DNAse I (Thermo Scientific) digested for 1 h, phenol-chloroform extracted, isopropanol precipitated and dissolved in 20 µl water. For C. elegans ~200 whole young adult hermaphrodites were washed 3x in PBS and lysed directly in Trizol by 30 cycles of sonication (30 s on, 30 s off) in a Bioruptor (Diagenode).
The EZ RNA Methylation Kit (Zymo Research) was used for bisulfite treatment and purification of converted RNA according to the instructions provided by the manufacturer. 400 ng RNA were reverse-transcribed using Super Script III reverse transcriptase (Life Technologies) and gene-specific reverse primers (see below) for 50 min following the manufacturer’s instructions. 5 µl cDNA was subjected to the following touchdown-PCR program in a 25 µl reaction with KAPA2G Robust Polymerase and Buffer A (Kapa Biosystems):  95°C  3 min  95°C  30 s*  55-45°C 30s*  *20 cycles, -0.5°C annealing per cycle   72°C  1 min*  95°C  30 s**  45°C  30 s**  **35 cycles  72°C  1 min**  72°C  5 min  PCR products were gel-purified using PCR- and Gel Extraction Kit (Favorgen) and eluded in 30 µl. 5 µl were subjected to a second round of PCR as above using barcoded primers and only 30 cycles in the second cycling step (**). Up to 24 barcoded samples were pooled to equal molarity and subjected to IonTorrent sequencing using a 314 Torrent Sequencing Chip Kit (Life Technologies).    Primer sequences (without barcode):  SC-25S-rRNA_bisulfite_sense: TGGTTAGAAAGTGATGTT  SC-25S-rRNA_bisulfite_as: TCTCATTAATCCATTCA  CE-28S-rRNA_bisulfite_sense: TGAATGTTAAATTGTAGTAATT  CE-28S-rRNA_bisulfite_as: TCTCGTTAATCCATTCA    For barcode sequences see "barcode" field in the SAMPLES section

treatment_protocol: S. cerevisiae: 0.4 mM H2O2 (only for stress conditions) and after 15 or 75 min, 125 µg/ml cycloheximide (Sigma) were added and the cells were incubated at the same temperature with shaking for further 15 min.

tag: h2o2 stress

value: 90 min 0.4 mM

tag: barcode

value: ATAGTAGTG


title: yeast rcm1 knockout, 30 min H2O2, monosomes

description: RNA monosome fraction

value: 30 min 0.4 mM

value: TGATACGTCT


title: BirAmVenusUbc6_sec66∆_+CHX_2minBiotin_input

description: ribosome protected mRNA fragment


title: H4-Ac_noStarv

value: H4 Ac (Millipore, 06-866 )


title: WCE_starved_DMSO

value: serum starved


title: BirAmVenusUbc6_+CHX_7minBiotin_pulldown

description: ribosome protected mRNA fragment

value: his3::pSEC63-BirA-mVenus-UBC6 TA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 leu2delta0


title: BirAmVenusUbc6_+CHX_7minBiotin_input

description: ribosome protected mRNA fragment


title: yeast rcm1 knockout, unstressed, monosomes

description: RNA monosome fraction

value: CTCGCGTGTC


title: yeast rcm1 knockout, unstressed, polysomes

description: RNA polysome fraction

value: CGTGTCTCTA


title: BirAmVenusUbc6_+CHX_2minBiotin_pulldown

description: ribosome protected mRNA fragment


title: yeast rcm1 knockout, 30 min H2O2, polysomes

description: RNA polysome fraction

value: TCTCTATGCG


title: yeast wild-type, 90 min H2O2, monosomes

description: RNA monosome fraction

value: wt

value: ATATCGCGAG


title: H3K27Ac_serum_DMSO

value: H3K27Ac ( abcam, ab4729)


title: H3K27Ac_serum_JQ1


title: Pol II_starved_DMSO

value: DMSO


title: Pol II_serum_DMSO

value: Pol II (Santa Cruz Biotechnology, N20, sc-899)


title: BirAHeh2Ssh1_+CHX_7minBiotin_replicate_input

description: ribosome protected mRNA fragment

value: ssh1::BirA-heh2-SSH1::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 his3delta1


title: yeast wild-type, 30 min H2O2, polysomes

description: RNA polysome fraction

value: AGACGCACTC


title: yeast wild-type, unstressed, monosomes

description: RNA monosome fraction

value: ACGCTCGACA


title: BirAmVenusSsh1_+CHX_2minBiotin_pulldown

description: ribosome protected mRNA fragment

value: ssh1::BirA-mVenus-SSH1::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 his3delta1


title: yeast wild-type, 90 min H2O2, polysomes

description: RNA polysome fraction

value: 90 min 0.4 mM

value: ATCAGACACG


title: yeast wild-type, 30 min H2O2, monosomes

description: RNA monosome fraction

value: 30 min 0.4 mM

value: AGCACTGTAG


title: CDK9_noStarv

value: continuous culture

value: CDK9 (Santa Cruz Biotechnology, sc-8338)


title: BirAmVenusSsh1_+CHX_2minBiotin_input

description: ribosome protected mRNA fragment


title: CKD9_serum_DMSO

value: serum starved and re-fed


title: BirAHeh2Ssh1_+CHX_7minBiotin_replicate_pulldown

description: ribosome protected mRNA fragment


title: BirAHeh2Ssh1_+CHX_7minBiotin_pulldown

description: ribosome protected mRNA fragment


title: yeast wild-type, unstressed, polysomes

description: RNA polysome fraction

value: ACGAGTGCGT


title: BirAHeh2Ssh1_+CHX_7minBiotin_input

description: ribosome protected mRNA fragment


title: CDK9_starved_DMSO

value: serum starved


title: CKD9_serum_JQ1


title: BRD4_serum_JQ1

value: BRD4 (C-terminus) made in house


title: BirAmCherrySec61beta_+CHX_10minBiotin_input

description: ribosome protected mRNA fragment

organism: Homo sapiens


title: BirA_+CHX_2minBiotin_input

description: ribosome protected mRNA fragment

value: rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI leu2::pPGK1-BirA::LEU2 ura3delta0 met15delta0 his3delta1


title: BirAmCherrySec61beta_+CHX_10minBiotin_pulldown

description: ribosome protected mRNA fragment


title: OrR_st12-13_Cdc45

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: OrR stage 12-13Cdc45 ChIP

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to the dm3 genome assembly using BWA using the default parameters with the exception of no gaps allowed (-o 0)
Data were filtered using the following specifications…
Peaks were called using MACS2 default settings and a p value of 10-3.
Genome_build: dm3
Supplementary_files_format_and_content: MACS peak files. Information include: chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region (e.g. pvalue =1e-10, then this value should be 100), fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage. Coordinates in .txt is 1-based which is different with BED format.

organism: Drosophila melanogaster

source_name: pooled stage 12 and 13 egg chambers

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media.Females were fattend for two days on wet yeast

extract_protocol:
Egg chambers were dounced and sonicated using a Biorupto 300 (Diagenode)
Libraries were constrcted using the NEB Next ChIP seq kit (Part # E6200S) according to manufactures recommendations with indexing primers for multiplexing

treatment_protocol: Ovaries were dissected into EBR mediumand  fixed in 2% formaldehyde. Ovaries were resuspended in LB3 and indiviudal egg chambers were isolated. When enough were collected (600 per ChIP reaction), ChIP was performed with either anti-SUUR, anti-Cdc45 or GP IgG

value: OrR

value: Cdc45 (made in-house)

tag: developmental stage

value: pooled stage 12 and 13

tag: tissue

value: egg chamber


title: BRD4_noStarv

value: DMSO


title: H3K27Ac_noStarv

value: H3K27Ac ( abcam, ab4729)


title: BirA_+CHX_2minBiotin_pulldown

description: ribosome protected mRNA fragment


title: OrR_st12-13_IgG

description: OrR stage 12-13 IgG ChIP

value: IgG (made in-house)


title: OrR_st12-13_SUUR

description: OrR stage 12-13 SUUR ChIP

value: SUUR (made in-house)


title: BRD4_serum_DMSO


title: BirAmVenusUbc6_+CHX_2minBiotin_input

description: ribosome protected mRNA fragment

value: his3::pSEC63-BirA-mVenus-UBC6 TA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 leu2delta0


title: H3K27Ac_starved_DMSO


title: BRD4_starved_DMSO


title: OrR_st12-13_Input

description: OrR stage 12-13 Input


title: Om45mVenusBirA_-CHX_2minBiotin_pulldown

description: ribosome protected mRNA fragment

data_processing:
Library strategy: ribosome profiling
base calls were called with Illumina CASAVA software (1.6-1.8)
3' adaptor was trimmed using a custom python script
reads were aligned sequentially first to rRNA, then unaligned reads were aligned to tRNA, then unaligned reads were aligned to a genomic index (sacCer3)
expression was quantitated using custom scripts after P-site mapping
Genome_build: sacCer3
Supplementary_files_format_and_content: tab delimited file containing gene annotations, count and rpkm data

growth_protocol: Yeast cells were grown in SD media containing 0.125 ng/ml D-biotin to OD600 .4-.6.

extract_protocol:
Cells were harvested by filtration, flash frozen, and cryogenically pulverized in a Retsch mixer-mill
Footprinting was performed with RNase I, monosomes purified on 10-50% sucrose gradients and biotinylated ribosomes purified on streptavidin dynabeads.  RNA was extracted with trizol and protected fragments gel purified.  Ends were repaired with T4 PNK and ligated to a pre-adenylated linker with T4 RNA Ligase 2.  Ligated fragments were gel purified, reverse transcribed and gel purified.  The cDNA was circularized then PCR amplified.

treatment_protocol: Where indicated, cells were treated with 100 µg/ml cycloheximide for 2 minutes prior to biotin induction for 2 minutes with 10 nM biotin.

value: om45::OM45-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI leu2::pPGK1-BirA::LEU2 ura3Δ0 met15Δ0 his3Δ1


title: Om45mVenusBirA_-CHX_2minBiotin_input

description: ribosome protected mRNA fragment


title: OrR_st10_Cdc45

description: OrR stage 10 Cdc45 ChIP

source_name: stage 10 egg chambers from OrR

value: stage 10


title: OrR_st10_IgG

description: OrR stage 10 IgG ChIP


title: PU.1 input

city: LONDON

first: Rodney

last: DeKoter

state: Ontario

address: 1151 Richmond street

department: Microbiology and Immunology

country: Canada

institute: University of Western Ontario

data_processing:
When .bam files were provided, bam files were converted to BAM/SAM to FASTQ using Galaxy tool v.  1.56.1
FASTQ files were aligned to MM9 using Map with Bowtie for Illumina v. 1.1.2 with the following configurations: Single-end library, first read not skipped, only align first n reads: off, no trimming -5 or -3, maximum number of mismatches permitting in the seed:2, Maximum permitted total of quality values at mismatched read positions: 70, Seed length:28, Whether or not to round to the nearest 10 and saturating at 30: 10, MAQ-like alignment policy, Regular mode for Tryhard Report up to n valid alignments per read:1, Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best):off, Maximum number of backtracks permitted when aligning a read (--maxbts): 125, Override the offrate of the index to n :off, Seed for pseudo-random number generator: default
Peaks for individual files were called usings MACS with a mappable genome size of 1910000000 bp (MM9). Input controls were used when available. Peaks were called with a tag size was set to either 75 (rep1)  or 100 (rep2), band widh of 300 and a Pvalue cutoff for peak detection of 1e-05. Peak Model was generated using an MFOLD high-confidence enrichment ratio against background of 15. Wiggle files were created using a resolution of 10bp.
Independant experiments were combined using mmChIP v. 1.0.0 with a mappable genome size of 1910000000  and a p-value cutoff for peak detection of 1e-05. Input .bed files for mmChip were generated using Convert from BAM to BED tool v0.1.0 in Galaxy.
Unique peaks were identified by subtracting intervals of Bed files and reporting intervals that did not have at least 1 bp overlap between datasets
Genome_build: MM9
Supplementary_files_format_and_content: .bed files were generated with MACS and represent regions of predicted binding sites. .wig files were generated concurrantly in MACS and represent signal for viewing in a genome browser

source_name: WEHI-279 mouse lymphoma cells

growth_protocol: Mouse WEHI-279 lymphoma cells were cultured (typically 1 million cells/10 ml media into a T75 flask) in complete DMEM medium (Multicell, 4.5g/L glucose) supplemented with 10% fetal bovine serum, 1x penicillin/streptomycin/L-glutamine, 5x10^-5 B-mercaptoethanol and 5mM HEPES buffer

extract_protocol:
Cell lysates were sonicated for 30 minutes and PU.1/Spi-B-DNA complexes were isolated with an anti-FLAG antibody.
Fragmented DNA was quantified using 2100 Bioanalyzer (Agilent Technologies). Libraries were generated robotically with 10 ng of fragmented DNA (range 100-300 bp) using the Kapa HTP Library Preparation Kit (Kapa Biosystems) as per the manufacturer’s recommendations except that adapters and PCR primers were diluted 100-fold,  the size selection step was done after the PCR step and the number of PCR cycles increased by 6. Adapters and PCR primers were purchased from Integrated DNA Technologies) whereas size selection has been performed on a Pippin Prep instrument (SAGE Biosciences Inc). Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (D-Mark). Average size fragment was determined using a LaChip GX (PerkinElmer) instrument.    Libraries were sequenced on a SR100 run on a HiSeq2000 (Illumina).

treatment_protocol: Cells were stably transfected to express 3x FLAG-tagged Spi-B or PU.1

tag: transcription factor

tag: antibody

tag: sample type

value: input control


title: Spib input


title: GM12878 GRO-seq

state: NY

description: cDNA (from nascent RNA)

data_processing:
Library strategy: GRO-Seq
Pass Filter: Reads that pass filter were selected from fastq files.
Read Trimming: Reads were trimmed to 30 bases.
rDNA filter: Reads were first mapped to a copy of rRNA gene (GenBank accession #: U13369.1) including external and internal spacers, and only reads that were not mapped to the rDNA were kept.
Mapping to the genome: Bowtie was used to map 30mers with up to two mismatches to the genome.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Processed data files are bigWigs of each sample. Each entry represents the number of reads at each base.

source_name: GM12878 cells

extract_protocol:
Nuclei isolation: All steps performed and buffers kept at 4oC. 10 mls of cells were spun down at 700g in a swinging bucket rotor for 5 min. Cells were washed in 1X cold PBS. Cells were washed in 10ml of buffer W (10mM Tris-Cl, pH 7.5, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, and 0.5 mM DTT). Cells were resuspended in 5mls of Buffer P (10mM Tris-Cl, pH 7.5, 10mM KCl, 250mM sucrose, 5mM MgCl2, 1mM EGTA, and 0.5 mM DTT, .05% tween-20 and/or .1% Igepal), and incubated 5 min. on ice. Permeabilized cells were washed twice in 5ml of buffer P, resuspended in 1ml of buffer P, and transferred to a 1.7ml eppendorf tube. Cells were pelleted at 1000 x g in a fixed angle rotor for 5min and then resuspended in 500 ml of buffer F (50 mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA, 0.5mM DTT). Cells were pelleted at 100g for 5 min, resuspended in 100 ml of buffer F, and then flash frozen in liquid nitrogen.
GRO-seq libraries were prepared as in Core et al. (Core, Waterfall, and Lis, 2008), with the following modifications. Trizol (Invitrogen) was used to stop the reaction instead of DNase I and proteinase K treatment. The RNA was further extracted once with acid phenol:chloroform, and once with chloroform before precipitating with 2.5 volumes of -20oC ethanol. Bead binding buffers all contained 4units/ml of SUPERaseIN (Ambion) and the following buffers were slightly modified. Bead blocking buffer: 0.25X SSPE, 1mM EDTA, 0.05% Tween, 0.1% PVP, and 1mg/ml ultrapure BSA (Ambion); Binding buffer: 0.25XSSPE, 37.5mM NaCl, 1mM EDTA, 0.05% tween; Low-salt wash buffer: 0.2X SSPE, 1mM EDTA, 0.05% Tween. High-salt wash buffer: 0.25% SSPE, 137.5mM NaCl, 1mM EDTA, 0.05% Tween. The end repair steps were modified as follows. Pelleted RNA from the first bead binding was resuspended in 20ul, and heated to 70oC for 5min, followed by incubation on ice for 2min. 1.5ul tobacco acid pyrophosphatase (TAP) buffer, 4.5ul water, 1 ul SUPERaseIn, and 1.5ul TAP (Epicentre) were then added and the reaction incubated at 37oC for 1.5 hours. 1ul 300mM MgCl2 and 1ul T4 polynucleotide Kinase (PNK) were added to the reaction for an additional protocols l 30 min. for phosphorylating the 5'-ends, 20ul T4 PNK buffer, 2ul 100mM ATP, 145ul water, 1ul SUPERaseIn, and an additional 2ul of PNK were added for 30 min at 37oC. The reaction was then stopped by addition of 20mM EDTA followed by acid phenol extraction and precipitation.

tag: cell line

tag: cell type

value: lymphoblastoid B-cell line

value: nuclear run-on

value: BrU

value: anti-BrU (Santa Cruz Biotechnology, sc-32323-ac, lot# I2111)


title: Om45mVenusBirA_+CHX_2minBiotin_pulldown

description: ribosome protected mRNA fragment


title: Spib rep2

value: SpiB

value: Monoclonal ANTI-FLAG M2 (F3165 SIGMA)

value: ChIP chromatin


title: Spib rep1


title: Om45mVenusBirA_+CHX_2minBiotin_input

description: ribosome protected mRNA fragment


title: OrR_st10_Input

description: OrR stage 10 Input

value: OrR


title: OrR_st10_SUUR

description: OrR stage 10 SUUR ChIP

value: egg chamber


title: PU.1 rep2


title: GM12878 GRO-cap control

description: cDNA (from nascent RNA)

data_processing:
Library strategy: GRO-cap
Pass Filter: Reads that pass filter were selected from fastq files.
Read Trimming: Reads were trimmed to 30 bases.
rDNA filter: Reads were first mapped to a copy of rRNA gene (GenBank accession #: U13369.1) including external and internal spacers, and only reads that were not mapped to the rDNA were kept.
Mapping to the genome: Bowtie was used to map 30mers with up to two mismatches to the genome.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Processed data files are bigWigs of each sample. Each entry represents the number of reads at each base.

source_name: GM12878 cells, not TAP treated

extract_protocol:
Nuclei isolation: All steps performed and buffers kept at 4oC. 10 mls of cells were spun down at 700g in a swinging bucket rotor for 5 min. Cells were washed in 1X cold PBS. Cells were washed in 10ml of buffer W (10mM Tris-Cl, pH 7.5, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, and 0.5 mM DTT). Cells were resuspended in 5mls of Buffer P (10mM Tris-Cl, pH 7.5, 10mM KCl, 250mM sucrose, 5mM MgCl2, 1mM EGTA, and 0.5 mM DTT, .05% tween-20 and/or .1% Igepal), and incubated 5 min. on ice. Permeabilized cells were washed twice in 5ml of buffer P, resuspended in 1ml of buffer P, and transferred to a 1.7ml eppendorf tube. Cells were pelleted at 1000 x g in a fixed angle rotor for 5min and then resuspended in 500 ml of buffer F (50 mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA, 0.5mM DTT). Cells were pelleted at 100g for 5 min, resuspended in 100 ml of buffer F, and then flash frozen in liquid nitrogen.
All NRO-reactions and bead enrichment steps for GRO-cap were carried out as described in GRO-seq, with the exception that the RNA for GRO-cap was not base hydrolyzed. After the first bead binding, the TruSeq RNA 3' Adapter (RA3) (Illumina part # 15013207) was ligated to the 3'-end of the NRO RNA. First, 50 pmoles of the 3'-adapter were mixed with NRO RNA, and 2 ml 50% PEG 8000, brought to 14 ml with DEPC water, incubated at 70°C for 3 min and put on ice for 2 min. Then, 2 ml of 10X T4 RNA Ligase I buffer, 2 ml 10 mM ATP, 1 ml SUPERaseIN, and 1.5 ml T4 RNA Ligase I (NEB, M0204) were added and reaction incubated at 22°C for 4-6 hr. The reaction was then brought to 100 ml with binding buffer and subjected to a second round of bead enrichment. After the second bead enrichment, 5' mono-phosphate RNAs were selected against in two successive steps. First, to selectively degrade RNAs with a 5'-mono-phosphate, NRO RNA was resuspended in 16.5 ml DEPC water, mixed with 0.5 ml SUPERaseIN, 2 ml 10X Terminator reaction buffer A, and 1 ml of Terminator 5'-phosphate-dependent exonuclease (Epicentre, TER51020), and incubated at 30°C for 1 hr. The reaction was extracted and precipitated using the standard method (above), and resupended in 10 ml DEPC water. Second, 5'-mono-phospate RNAs were deposphorylated to prevent their participation in subsequent ligation reactions. For this, the RNA was then mixed with 1 ml SUPERaseIN, 14.5 ml DEPC water, 10X Antarctic Phosphatase buffer, 1.5 ml of Antarctic Phosphatase (NEB, M0289S), and incubated at 37°C for 30 min. The reaction was brought to 200 ml with 10 mM Tris-HCl (pH 7.5), 5 mM EDTA, and heat inactivated at 65°C for 5 min. The reaction was then extracted and precipitated using the standard extraction method and resuspended in 10 ml DEPC water. The 5'-capped RNAs then were prepared for ligation and the final library preparation steps. The NRO RNAs were then split in half and the experimental sample was treated with Tobacco Acid Pyrophosphatase (TAP): 1 ml SUPERaseIN, 15 ml DEPC water, 3 ml 10X TAP buffer, and 1 ml TAP (Epicentre, T19500), incubation at 37°C for 1 hr. The control reaction was treated identically except for the addition of TAP. The reaction was brought to 200 ml and then extracted and precipitated using the standard method. The TruSeq RNA 5' Adapter (RA5), (Illumina part # 15013205) was ligated to the 5'-end of the NRO RNA. First, 50 pmoles of the 5'-adapter were mixed with NRO RNA, and 2 ml 50% PEG 8000, brought to 14 ml with DEPC water, incubated at 70°C for 3 min and put on ice for 2 min. Then, 2 ml of 10X T4 RNA Ligase I buffer, 2 ml 10 mM ATP, 1 ml SUPERaseIN, and 1.5 ml T4 RNA Ligase I (NEB, M0204) were added and reaction incubated at 22°C for 4-6 hr. The reaction was then brought to 100 ml with binding buffer and subjected to a third round of bead enrichment. After the third enrichment, samples were reverse transcribed, amplified and PAGE purified and quantified before submission for sequencing.

tag: rna source

tag: pull-down strategy

tag: tap treated

value: no


title: PU.1 rep1


title: SuUR_gamma-H2Av

description: SuUR 3SG gamma-H2Av ChIP

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to the dm3 genome assembly using BWA using the default parameters with the exception of no gaps allowed (-o 0)
Data were filtered using the following specifications…
Peaks were called using MACS v1.4 with the following setting; -tsize=40 --wig --space=25 --mfold=10,30 --pvalue=1e-5. Peaks were further filtered based on the FDR. Peaks with a FDR of <5% were included in the analysis
Genome_build: dm3
Supplementary_files_format_and_content: MACS peak files. Information include: chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region (e.g. pvalue =1e-10, then this value should be 100), fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage. Coordinates in .txt is 1-based which is different with BED format.

source_name: third instar salivary gland from SuUR

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media.

extract_protocol:
Salivary glands were dounced and sonicated using a Biorupto 300 (Diagenode)
Libraries were constrcted using the NEB Next ChIP seq kit (Part # E6200S) according to manufactures recommendations with indexing primers for multiplexing

treatment_protocol: Salivary glands were hand dissected from committed wandering third instar larvae directly into EBR medium and frozen within less than 30 min in liquid nitrogen. When enough were collected, ChIP was performed with either anti gamma-H2Av antibody (Rockland) or rabbit IgG (Abcam)

value: SuUR

value: gamma-H2Av (Rockland)

value: third instar

value: salivary gland


title: WT Liver Input

city: Houston

first: Erin

last: Stashi

state: TX

address: One Baylor Plaza

institute: Bayolor College of Medicine

description: Sample 4

data_processing:
Approximately 24 Million reads identified by Illumina’s Genome Analyzer 2 were mapped to the mouse genome (Build37.1/mm9) using the ELAND software
Only the sequences uniquely mapped with no more than 2 mismatches in the first 28 bp were kept and used as valid reads
Peak calling was carried out by MACS 1.3.7.1 (option: p-value=1E-10 and MFOLD 30) were used
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files reporting called peaks

source_name: Liver

extract_protocol:
Liver was extracted and flash frozen in liquid nitrogen.
The library construction was performed by Active Motif according to their protocol.

value: Liver

value: Adult

tag: gender

value: Male

tag: genotype/variation

value: WT

value: none (input)


title: OrR_rabbit_IgG

description: OrR 3SG rabbit IgG ChIP

source_name: third instar salivary gland from OrR

tag: chip antibody

value: IgG (Abcam)


title: SRC-2 KO

description: Sample 3

value: SRC-2 KO

value: SRC-2  antibody (Bethyl Laboratories, catalog number A300-346, lot number A-1)


title: SuUR_Input

description: SuUR 3SG Input


title: K562 GRO-cap control

description: cDNA (from nascent RNA)

source_name: K562 cells, not TAP treated

value: chronic myelogenous leukemic cell line

value: nuclear run-on

value: BrU

value: anti-BrU (Santa Cruz Biotechnology, sc-32323-ac, lot# I2111)


title: G9a/GLP double knockout MOE

first: Stavros

last: Lomvardas

institute: Univ of California - SF

description:
rna-seq data
g9aGlp_cuffdiff.xlsx

data_processing:
map fastq with tophat to generate .bam
Quantify expression with cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff – rpkm values per genotype

molecule: polyA RNA

source_name: olfactory epithelium from E18.5 mouse embryo

growth_protocol: mice with mixed genetic background

extract_protocol:
trizol followed by polyA purification with polydT magnetic beads
scriptseq V2 (illumina/epicentre)

value: mixed background originating chiefly from C57/B6

tag: genotype

value: G9a/GLP double knockout


title: g9a KO GLP heterozygote MOE

description:
rna-seq data
g9aGlp_cuffdiff.xlsx

tag: strain

value: g9a KO GLP heterozygote

value: olfactory epithelium from E18.5 mouse embryo


title: SRC-2 ZT18

description: Sample 2

tag: time


title: K562 GRO-cap

description: cDNA (from nascent RNA)

source_name: K562 cells, TAP treated

value: yes


title: GM12878 GRO-cap

description: cDNA (from nascent RNA)

source_name: GM12878 cells, TAP treated

value: lymphoblastoid B-cell line


title: OrR_gamma-H2Av

description: OrR 3SG gamma-H2Av ChIP

value: OrR

value: gamma-H2Av (Rockland)

value: third instar

value: salivary gland


title: g9a knockout MOE

description:
rna-seq data
g9aGlp_cuffdiff.xlsx

value: g9a knockout


title: OrR_Input

description: OrR 3SG Input


title: SRC-2 ZT4

description: Sample 1

value: Liver

value: Adult

value: Male

value: WT


title: g9a heterozygote MOE

description:
rna-seq data
g9aGlp_cuffdiff.xlsx

value: g9a heterozygote


title: R_RNA_290-96

status: Public on Nov 09 2014

city: Ann Arbor

first: Xiang

last: Zhou

state: MI

address: 1415 Washington Heights

department: Biostatistics

institute: UNIVERSITY OF MICHIGAN

description: RNA-seq for Rhesus Macaque Individual 290-96 Mm290-96

data_processing:
Basecalls by Illumina CASAVA 1.7.0
Mapped reads to panTro3 and rheMac2 using BWA 0.5.9, allowing up to 2 mismatches per read (-n 2), and excluding gapped alignments (-o 0)
Discarded reads that were assigned with a quality score less than 10 or were duplicates
For Chip-Seq, MACS version 1.4.1 was used to identify sharp peaks of enrichment for H3K4me1, H3K4me3, H3K27ac, and Pol II; RSEG version 0.4.4 was used to classify enrichment of broad genomic regions of enrichment for H3K27me3
For RNA-seq, reads mapped to orthologous exons are counted and summed at gene level
For Chip-Seq, a two-step procedure is used to classify the enriched regions/peaks for each mark
Genome_build: panTro3 and rheMac2 (and hg19 for H_input)
Supplementary_files_format_and_content: bed file format; for ChipSeq they contain peaks and enriched regions identified for each marker; for RNA-seq, they contain number of reads mapped to each gene

organism: Macaca mulatta

source_name: lymphoblastoid cell line

growth_protocol: cell line source: LCLs from chimpanzee and rhesus macaque individuals were obtained from New Iberia Research Center (University of Louisiana at Lafayette), and New England Primate Research Center (NEPRC, Harvard Medical School)

extract_protocol:
RNA was extracted from each LCL sample using a Qiagen RNeasy mini kit. High quality of the RNA was confirmed using Agilent's 2100 Bioanalyzer (RIN ≥ 9.3 for all samples)
Samples for RNA sequencing were prepared as previously described (Marioni et al. Genome Research 2008). Each sample was sequenced in one lane of an Illumina GAII flow cell.

value: lymphoblastoid

tag: Sex


title: R_RNA_265-95

description: RNA-seq for Rhesus Macaque Individual 265-95 Mm265-95


title: R_RNA_249-97

description: RNA-seq for Rhesus Macaque Individual 249-97 Mm249-97


title: R_RNA_256-95

description: RNA-seq for Rhesus Macaque Individual 256-95 Mm256-95


title: R_RNA_173-02

description: RNA-seq for Rhesus Macaque Individual 173-02 Mm173-02

value: Female


title: R_RNA_153-99

description: RNA-seq for Rhesus Macaque Individual 153-99 Mm153-99


title: R_H3K27me3_290-96

description: H3K27me3 ChIP-seq for Rhesus Macaque Individual 290-96 Mm290-96

extract_protocol:
Chromatin was extracted using protocol described in Cain et al. 2011, except that for some samples, chromatin was sheared with a Covaris S2 (settings: 40 minutes, duty cycle 20%, intensity 8, 200 cycles/burst, 500uL at a time in 12 x 24mm tubes).
Prepared Illumina sequencing libraries as described by the ENCODE Project Consortium (2011), starting with 20 uL of ChIP output or 4 ng of pooled input sample.

value: H3K27me3 antibody (4 ug, Millipore 07-449)


title: R_H3K27me3_173-02

description: H3K27me3 ChIP-seq for Rhesus Macaque Individual 173-02 Mm173-02


title: R_H3K27me3_265-95

description: H3K27me3 ChIP-seq for Rhesus Macaque Individual 265-95 Mm265-95


title: R_H3K27ac_290-96

description: H3K27ac ChIP-seq for Rhesus Macaque Individual 290-96 Mm290-96

value: H3K27ac antibody (4 ug, Abcam ab4729)


title: R_H3K27me3_153-99

description: H3K27me3 ChIP-seq for Rhesus Macaque Individual 153-99 Mm153-99


title: R_H3K27me3_181-96

description: H3K27me3 ChIP-seq for Rhesus Macaque Individual 181-96 Mm181-96


title: R_H3K27me3_249-97

description: H3K27me3 ChIP-seq for Rhesus Macaque Individual 249-97 Mm249-97


title: R_H3K27me3_150-99

description: H3K27me3 ChIP-seq for Rhesus Macaque Individual 150-99 mM150-99


title: R_RNA_181-96

description: RNA-seq for Rhesus Macaque Individual 181-96 Mm181-96


title: R_H3K27ac_153-99

description: H3K27ac ChIP-seq for Rhesus Macaque Individual 153-99 Mm153-99


title: R_H3K27ac_265-95

description: H3K27ac ChIP-seq for Rhesus Macaque Individual 265-95 Mm265-95


title: R_H3K27ac_256-95

description: H3K27ac ChIP-seq for Rhesus Macaque Individual 256-95 Mm256-95


title: R_H3K4me3_256-95

description: H3K4me3 ChIP-seq for Rhesus Macaque Individual 256-95 Mm256-95

value: H3K4me3 antibody (4 ug, Abcam ab8580)


title: R_H3K27ac_173-02

description: H3K27ac ChIP-seq for Rhesus Macaque Individual 173-02 Mm173-02


title: R_H3K27ac_150-99

description: H3K27ac ChIP-seq for Rhesus Macaque Individual 150-99 mM150-99


title: R_H3K27ac_249-97

description: H3K27ac ChIP-seq for Rhesus Macaque Individual 249-97 Mm249-97


title: R_H3K4me3_249-97

description: H3K4me3 ChIP-seq for Rhesus Macaque Individual 249-97 Mm249-97


title: R_RNA_150-99

description: RNA-seq for Rhesus Macaque Individual 150-99 mM150-99


title: R_H3K4me3_181-96

description: H3K4me3 ChIP-seq for Rhesus Macaque Individual 181-96 Mm181-96


title: R_H3K4me3_290-96

description: H3K4me3 ChIP-seq for Rhesus Macaque Individual 290-96 Mm290-96


title: R_H3K4me3_173-02

description: H3K4me3 ChIP-seq for Rhesus Macaque Individual 173-02 Mm173-02


title: R_H3K4me3_150-99

description: H3K4me3 ChIP-seq for Rhesus Macaque Individual 150-99 mM150-99


title: R_H3K4me1_265-95

description: H3K4me1 ChIP-seq for Rhesus Macaque Individual 265-95 Mm265-95

value: H3K4me1 (12 ug, Millipore 07-436)


title: R_H3K4me1_290-96

description: H3K4me1 ChIP-seq for Rhesus Macaque Individual 290-96 Mm290-96


title: R_H3K4me1_249-97

description: H3K4me1 ChIP-seq for Rhesus Macaque Individual 249-97 Mm249-97


title: R_H3K27me3_256-95

description: H3K27me3 ChIP-seq for Rhesus Macaque Individual 256-95 Mm256-95


title: R_H3K4me3_153-99

description: H3K4me3 ChIP-seq for Rhesus Macaque Individual 153-99 Mm153-99


title: R_H3K4me1_181-96

description: H3K4me1 ChIP-seq for Rhesus Macaque Individual 181-96 Mm181-96


title: R_H3K4me1_173-02

description: H3K4me1 ChIP-seq for Rhesus Macaque Individual 173-02 Mm173-02


title: R_H3K4me3_265-95

description: H3K4me3 ChIP-seq for Rhesus Macaque Individual 265-95 Mm265-95


title: R_H3K4me1_153-99

description: H3K4me1 ChIP-seq for Rhesus Macaque Individual 153-99 Mm153-99


title: R_H3K4me1_150-99

description: H3K4me1 ChIP-seq for Rhesus Macaque Individual 150-99 mM150-99


title: C_RNA_Pt30

description: RNA-seq for Chimpanzee Individual Pt30 Min19919

organism: Pan troglodytes


title: C_RNA_Pt91

description: RNA-seq for Chimpanzee Individual Pt91 Min19913


title: C_RNA_3641

description: RNA-seq for Chimpanzee Individual 3641 S003641


title: C_RNA_4973

description: RNA-seq for Chimpanzee Individual 4973 S004973


title: C_H3K27me3_Pt30

description: H3K27me3 ChIP-seq for Chimpanzee Individual Pt30 Min19919


title: C_RNA_18358

description: RNA-seq for Chimpanzee Individual 18358 AG18358


title: C_H3K27me3_Pt91

description: H3K27me3 ChIP-seq for Chimpanzee Individual Pt91 Min19913


title: C_H3K27me3_4973

description: H3K27me3 ChIP-seq for Chimpanzee Individual 4973 S004973


title: C_RNA_3610

description: RNA-seq for Chimpanzee Individual 3610 S003610


title: C_RNA_18359

description: RNA-seq for Chimpanzee Individual 18359 AG18359


title: C_H3K27me3_3659

description: H3K27me3 ChIP-seq for Chimpanzee Individual 3659 S003659


title: C_H3K27me3_3641

description: H3K27me3 ChIP-seq for Chimpanzee Individual 3641 S003641


title: C_H3K27ac_Pt91

description: H3K27ac ChIP-seq for Chimpanzee Individual Pt91 Min19913


title: C_H3K27me3_18358

description: H3K27me3 ChIP-seq for Chimpanzee Individual 18358 AG18358


title: C_H3K27me3_3610

description: H3K27me3 ChIP-seq for Chimpanzee Individual 3610 S003610


title: C_H3K27me3_18359

description: H3K27me3 ChIP-seq for Chimpanzee Individual 18359 AG18359


title: R_H3K4me1_256-95

description: H3K4me1 ChIP-seq for Rhesus Macaque Individual 256-95 Mm256-95


title: C_H3K27ac_Pt30

description: H3K27ac ChIP-seq for Chimpanzee Individual Pt30 Min19919


title: C_H3K27ac_4973

description: H3K27ac ChIP-seq for Chimpanzee Individual 4973 S004973


title: C_H3K27ac_3641

description: H3K27ac ChIP-seq for Chimpanzee Individual 3641 S003641


title: C_H3K27ac_18359

description: H3K27ac ChIP-seq for Chimpanzee Individual 18359 AG18359


title: C_H3K27ac_18358

description: H3K27ac ChIP-seq for Chimpanzee Individual 18358 AG18358


title: C_RNA_3659

description: RNA-seq for Chimpanzee Individual 3659 S003659


title: C_H3K4me3_Pt30

description: H3K4me3 ChIP-seq for Chimpanzee Individual Pt30 Min19919


title: C_H3K4me3_3659

description: H3K4me3 ChIP-seq for Chimpanzee Individual 3659 S003659


title: C_H3K4me3_4973

description: H3K4me3 ChIP-seq for Chimpanzee Individual 4973 S004973


title: C_H3K4me3_3641

description: H3K4me3 ChIP-seq for Chimpanzee Individual 3641 S003641


title: C_H3K27ac_3610

description: H3K27ac ChIP-seq for Chimpanzee Individual 3610 S003610


title: C_H3K4me3_3610

description: H3K4me3 ChIP-seq for Chimpanzee Individual 3610 S003610


title: C_H3K4me3_18358

description: H3K4me3 ChIP-seq for Chimpanzee Individual 18358 AG18358


title: C_H3K4me3_18359

description: H3K4me3 ChIP-seq for Chimpanzee Individual 18359 AG18359


title: C_H3K4me1_Pt91

description: H3K4me1 ChIP-seq for Chimpanzee Individual Pt91 Min19913


title: C_H3K4me1_4973

description: H3K4me1 ChIP-seq for Chimpanzee Individual 4973 S004973


title: C_H3K4me1_Pt30

description: H3K4me1 ChIP-seq for Chimpanzee Individual Pt30 Min19919


title: R_PolII_290-96

description: PolII ChIP-seq for Rhesus Macaque Individual 290-96 Mm290-96

value: Pol II antibody (10 ug, Santa Cruz sc-9001)


title: C_H3K4me1_3659

description: H3K4me1 ChIP-seq for Chimpanzee Individual 3659 S003659


title: C_H3K4me1_18359

description: H3K4me1 ChIP-seq for Chimpanzee Individual 18359 AG18359


title: C_H3K4me1_3641

description: H3K4me1 ChIP-seq for Chimpanzee Individual 3641 S003641


title: R_PolII_256-95

description: PolII ChIP-seq for Rhesus Macaque Individual 256-95 Mm256-95


title: R_PolII_173-02

description: PolII ChIP-seq for Rhesus Macaque Individual 173-02 Mm173-02


title: R_PolII_249-97

description: PolII ChIP-seq for Rhesus Macaque Individual 249-97 Mm249-97


title: C_H3K4me1_3610

description: H3K4me1 ChIP-seq for Chimpanzee Individual 3610 S003610


title: C_H3K27ac_3659

description: H3K27ac ChIP-seq for Chimpanzee Individual 3659 S003659


title: R_PolII_150-99

description: PolII ChIP-seq for Rhesus Macaque Individual 150-99 mM150-99


title: R_PolII_153-99

description: PolII ChIP-seq for Rhesus Macaque Individual 153-99 Mm153-99


title: R_PolII_181-96

description: PolII ChIP-seq for Rhesus Macaque Individual 181-96 Mm181-96


title: C_input

description: Control ChIP-seq for Chimpanzee Pooled Individuals

value: pooled sample from all individuals


title: C_H3K4me3_Pt91

description: H3K4me3 ChIP-seq for Chimpanzee Individual Pt91 Min19913


title: C_PolII_Pt91

description: PolII ChIP-seq for Chimpanzee Individual Pt91 Min19913


title: R_input

description: Control ChIP-seq for Rhesus Macaque Pooled Individuals


title: C_PolII_3659

description: PolII ChIP-seq for Chimpanzee Individual 3659 S003659


title: seq-NA_N2_LTemb_Lemb4B

city: Chapel Hill

first: Tristan

last: De Buysscher

state: NC

address: CB# 3280, Coker Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description: input DNA

data_processing: BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse. Genome build: ce6

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Worm_embryo_growth_and_harvest_vSS7. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Embryos were incubated for 3.5 hours in M9 then frozen in liquid nitrogen. http://wiki.modencode.org/project/index.php/Worm_embryo_growth_and_harvest:JL:SS7

extract_protocol: Libraries were prepared according to Illumina's instructions for "Preparing Samples for ChIP Sequencing of DNA", with some variation. DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 DNA polymerase.  A's were then added to the 3' ends of the fragments using Kelow fragment (3'  5' exo minus). Paired-end adapters were then ligated onto the ends of the fragments.  DNA library was size selected by gel purification, fragments of 250-500 bp were band isolated from an agarose gel. DNA was PCR amplified for 18 cycles. The Bioanalyzer was used to verify fragment purification and quantify DNA.

treatment_protocol: Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in a Diagenode Bioruptor (40 pulses of 30 seconds with 1 minute rests in between at full power). Extracts are then spun down and the soluble fraction is stored for quality tests and future ChIP. http://wiki.modencode.org/project/index.php/Worm_popcorn_chromatin_extract_protocol_vSS1:JL:1

tag: Stage


title: R_PolII_265-95

description: PolII ChIP-seq for Rhesus Macaque Individual 265-95 Mm265-95


title: seq-NA_N2_LTemb_Lemb4C

description: input DNA


title: seq-NA_N2_LTemb_Lemb3B

description: input DNA


title: seq-NA_N2_LTemb_Lemb3A

description: input DNA


title: C_PolII_3610

description: PolII ChIP-seq for Chimpanzee Individual 3610 S003610


title: C_PolII_3641

description: PolII ChIP-seq for Chimpanzee Individual 3641 S003641


title: C_PolII_4973

description: PolII ChIP-seq for Chimpanzee Individual 4973 S004973


title: C_H3K4me1_18358

description: H3K4me1 ChIP-seq for Chimpanzee Individual 18358 AG18358


title: seq-NA_N2_LTemb_Lemb2

description: input DNA


title: C_PolII_18358

description: PolII ChIP-seq for Chimpanzee Individual 18358 AG18358


title: C_PolII_18359

description: PolII ChIP-seq for Chimpanzee Individual 18359 AG18359


title: H_input

description: Control ChIP-seq for Human Pooled Individuals

growth_protocol:
cell line source: LCLs from human individuals were obtained from Coriell Institute (http://www.coriell.org/); individual IDs are described in GEO GSE47991
Cell lines were grown at 37°C in RPMI media with 15% FBS, supplemented with 2 mM l-glutamate, 100 I.U./mL penicillin, and 100 Âµg/mL streptomycin.


title: LLAM1_C4toC2_T540m_2013_BR2

status: Public on Nov 08 2014

city: East Lansing

first: Nathan

middle: M

last: Good

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Quality filtering of raw reads was performed using Illumina's CASAVA
Reads were aligned to M. extorquens AM1 genome (MAGE, March 2nd, 2012) using BWA v.0.7.4-r385 with default parameters
Alignments were post-processed into sorted BAM files with SAMTools version 0.1.19-44428cd
Reads were attributed to open reading frames (ORFs) using htseq-count from the 'Htseq' framework version 0.5.4p5 in the 'intersection-nonempty' mode
Final abundance was measured by RPKM
Genome_build: MAGE, March 2nd, 2012
Supplementary_files_format_and_content: text file with RPKM values

organism: Methylorubrum extorquens AM1

source_name: Methylobacterium extorquens AM1_T540

growth_protocol: Succinate-limited chemostat cultures of wild-type Methylobacterium extorquens AM1 were grown with a dilution rate of 0.163 h^-1. After reaching steady-state, chemostat flows were stopped and 20 uM ethylamine was added to the bioreactor.

extract_protocol:
RNA was extracted as reported in Okubo, 2007
Libraries were constructed according to Illumina's instructions and performed by UW High Throughput Genomics Center (HTGC)

tag: timepoint


title: LLAM1_C4toC2_T1350m_2013_BR2

source_name: Methylobacterium extorquens AM1_T1350


title: LLAM1_C4toC2_T0_2013_BR2

source_name: Methylobacterium extorquens AM1_T0


title: LLAM1_C4toC2_T540m_2013_BR1


title: LLAM1_C4toC2_T1080m_2013_BR1

source_name: Methylobacterium extorquens AM1_T1080


title: LLAM1_C4toC2_T1080m_2013_BR2


title: LLAM1_C4toC2_T120m_2013_BR2

source_name: Methylobacterium extorquens AM1_T120


title: LLAM1_C4toC2_T0_2013_BR1


title: LLAM1_C4toC2_T120m_2013_BR1


title: miRi50

city: Leiden

first: Peter

middle: J. K.

last: Kuppen

address: PO Box 9600

department: Surgery

country: Netherlands

institute: Leiden University Medical Center

description:
miRNA
Processed data file column miRi50

data_processing:
3'-library adapters were removed from the sequences.
Remaining reads with at least 15 bases were aligned to the human hg19 reference genome using the Bowtie short-read aligner, allowing for up to three loci with two mismatches.
Crossmapping correction was applied to the alignments.
Aligned sequence tags were annotated based on the miRBase v19 release, resulting in separate expression values for the 5' and 3' mature miRNAs from the hairpin precursors.
Counts were subsequently transformed to counts per million.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file contains all annotated miRNA isoforms in rows and all samples in columns. Given are the read counts for each annotated miRNA isoform per sample.

source_name: primary colon adenocarcinoma, no metachronous metastasis

extract_protocol:
Small RNAs were isolated from laser capture microdissected tumor tissues using the Just-a-TubeTM RNA Isolation Kit.
Adapters were hybridized and ligated to isolated small RNAs. After reverse transcription, a flowcell adapter PCR (with a universal forward primer and fourteen available reverse primers) was performed to amplify and to apply a unique barcode to each sample within a sample-pool. Subsequently, samples were pooled into 4 pools in equimolar volumes of 2nM.

tag: tissue

value: primary colon adenocarcinoma

tag: tnm-stage

value: TNM-stage III

tag: age at surgery (yr)

value: male

tag: metastasis status

value: no metachronous metastasis


title: C_PolII_Pt30

description: PolII ChIP-seq for Chimpanzee Individual Pt30 Min19919

tag: cell line

tag: antibody


title: miRi49

description:
miRNA
Processed data file column miRi49

source_name: primary colon adenocarcinoma, metachronous metastasis

value: female

value: metachronous metastasis


title: miRi48

description:
miRNA
Processed data file column miRi48


title: P180 TSA Occipital Cortex Sample 2

city: New Haven

first: Pasko

last: Rakic

state: CT

address: 333 Cedar Street

department: Neurobiology

institute: Yale University

data_processing:
Reads trimmed and mapped using TopHat
TopHat .bam file converted to .sam
.sam file converted to .mrf
mrfQuantifier used to generate RPKMs for genes for each sample
.RPKM files for each sample concatenated into one .fpkm_tracking file
Genome_build: mm9
Supplementary_files_format_and_content: .fpkm_tracking contains FPKMs listed by gene for all samples

source_name: Mouse Brain Tissue

extract_protocol:
Samples were dissected into RLT buffer with 10% Beta-mercaptoethanol, disrupted and purified with a Qiagen micro-kit as per the manufacturers instructions
Libraries were prepared according to the standard Illumina protocol

value: Occipital Cortex

tag: treatment

value: TSA

tag: age


title: P180 TSA Olfactory Bulb Sample 2

value: Olfactory Bulb


title: P180 TSA Frontal Cortex Sample 2

value: Frontal Cortex


title: miRi46

description:
miRNA
Processed data file column miRi46

value: TNM-stage II

tag: gender


title: miRi45

description:
miRNA
Processed data file column miRi45


title: P180 TSA Occipital Cortex Sample 1


title: P180 TSA Olfactory Bulb Sample 1


title: LLAM1_C4toC2_T1350m_2013_BR1


title: P180 TSA Hippocampus Sample 1

value: Hippocampus


title: P180 TSA Frontal Cortex Sample 1


title: miRi44

description:
miRNA
Processed data file column miRi44


title: miRi43

description:
miRNA
Processed data file column miRi43


title: P180 Control Hippocampus Sample 2


title: LLAM1_C4toC2_T270m_2013_BR2

source_name: Methylobacterium extorquens AM1_T270


title: LLAM1_C4toC2_T270m_2013_BR1


title: P180 Control Olfactory Bulb Sample 2


title: miRi42

description:
miRNA
Processed data file column miRi42


title: P180 Control Hippocampus Sample 1


title: P180 Control Occipital Cortex Sample 2


title: P180 Control Frontal Cortex Sample 2


title: miRi41

description:
miRNA
Processed data file column miRi41


title: P180 Control Occipital Cortex Sample 1


title: miRi40

description:
miRNA
Processed data file column miRi40


title: P180 TSA Occipital Cortex Layer 6 Sample 2

value: Occipital Cortex Layer


title: P180 Control Olfactory Bulb Sample 1


title: P180 TSA Hippocampus Sample 2


title: miRi47

description:
miRNA
Processed data file column miRi47


title: miRi39

description:
miRNA
Processed data file column miRi39


title: P180 Control Frontal Cortex Sample 1


title: P180 TSA Occipital Cortex Layer 4 Sample 2


title: P180 TSA Occipital Cortex Layer 2 Sample 2


title: miRi37

description:
miRNA
Processed data file column miRi37


title: miRi38

description:
miRNA
Processed data file column miRi38


title: P180 TSA Occipital Cortex Layer 5 Sample 2


title: P180 TSA Occipital Cortex Layer 5 Sample 1


title: P180 TSA Occipital Cortex Layer 6 Sample 1


title: P180 TSA Occipital Cortex Layer 2 Sample 1


title: miRi36

description:
miRNA
Processed data file column miRi36


title: P180 Control Occipital Cortex Layer 4 Sample 2


title: P180 Control Occipital Cortex Layer 6 Sample 2


title: miRi35

description:
miRNA
Processed data file column miRi35


title: P180 TSA Occipital Cortex Layer 4 Sample 1


title: P180 Control Occipital Cortex Layer 2 Sample 1


title: P180 Control Occipital Cortex Layer 2 Sample 2


title: P180 Control Occipital Cortex Layer 5 Sample 1


title: miRi31

description:
miRNA
Processed data file column miRi31


title: miRi34

description:
miRNA
Processed data file column miRi34


title: miRi32

description:
miRNA
Processed data file column miRi32


title: P180 Control Occipital Cortex Layer 6 Sample 1


title: miRi33

description:
miRNA
Processed data file column miRi33


title: P26 Occipital Cortex Layer 6 Sample 1


title: P26 Occipital Cortex Layer 5 Sample 1


title: miRi30

description:
miRNA
Processed data file column miRi30


title: P26 Occipital Cortex Layer 4 Sample 1


title: P26 Occipital Cortex Layer 2 Sample 1


title: miRi29

description:
miRNA
Processed data file column miRi29


title: P180 TSA Frontal Cortex Layer 6 Sample 2

value: Frontal Cortex Layer


title: miRi28

description:
miRNA
Processed data file column miRi28


title: P180 TSA Frontal Cortex Layer 2 Sample 2


title: P180 TSA Frontal Cortex Layer 5 Sample 2


title: P180 TSA Frontal Cortex Layer 4 Sample 2


title: miRi27

description:
miRNA
Processed data file column miRi27


title: P180 Control Occipital Cortex Layer 5 Sample 2


title: P180 TSA Frontal Cortex Layer 5 Sample 1


title: miRi26

description:
miRNA
Processed data file column miRi26


title: P180 TSA Frontal Cortex Layer 4 Sample 1


title: P180 TSA Frontal Cortex Layer 2 Sample 1


title: P26 Occipital Cortex Layer 6 Sample 2


title: P180 Control Occipital Cortex Layer 4 Sample 1


title: P26 Occipital Cortex Layer 5 Sample 2


title: miRi25

description:
miRNA
Processed data file column miRi25


title: P26 Occipital Cortex Layer 4 Sample 2


title: miRi24

description:
miRNA
Processed data file column miRi24


title: miRi23

description:
miRNA
Processed data file column miRi23


title: P26 Occipital Cortex Layer 2 Sample 2


title: P180 Control Frontal Cortex Layer 6 Sample 2


title: P180 Control Frontal Cortex Layer 6 Sample 1


title: miRi21

description:
miRNA
Processed data file column miRi21


title: P180 Control Frontal Cortex Layer 5 Sample 1


title: P180 Control Frontal Cortex Layer 4 Sample 2


title: miRi20

description:
miRNA
Processed data file column miRi20


title: P180 Control Frontal Cortex Layer 4 Sample 1


title: P180 Control Frontal Cortex Layer 2 Sample 1


title: miRi19

description:
miRNA
Processed data file column miRi19


title: miRi17

description:
miRNA
Processed data file column miRi17


title: P180 TSA Frontal Cortex Layer 6 Sample 1


title: miRi16

description:
miRNA
Processed data file column miRi16


title: miRi14

description:
miRNA
Processed data file column miRi14


title: miRi15

description:
miRNA
Processed data file column miRi15


title: miRi11

description:
miRNA
Processed data file column miRi11


title: miRi12

description:
miRNA
Processed data file column miRi12


title: miRi09

description:
miRNA
Processed data file column miRi09


title: miRi13

description:
miRNA
Processed data file column miRi13


title: miRi10

description:
miRNA
Processed data file column miRi10


title: miRi08

description:
miRNA
Processed data file column miRi08


title: P180 Control Frontal Cortex Layer 5 Sample 2


title: miRi22

description:
miRNA
Processed data file column miRi22


title: P180 Control Frontal Cortex Layer 2 Sample 2


title: miRi06

description:
miRNA
Processed data file column miRi06


title: miRi04

description:
miRNA
Processed data file column miRi04


title: miRi05

description:
miRNA
Processed data file column miRi05


title: miRi07

description:
miRNA
Processed data file column miRi07


title: miRi01

description:
miRNA
Processed data file column miRi01


title: miRi18

description:
miRNA
Processed data file column miRi18


title: Dsim_MOF

status: Public on Nov 07 2014

city: Umeå

first: Jan

last: Larsson

state: Västerbotten

address: University Hospital, buildings 6 K and 6 L

department: Molecular Biology

country: Sweden

institute: Umeå University

description: ChIP-seq

data_processing:
Alignment to : Applied Biosystems Bioscope software v1.2.1
Enrichment ratio calculation: Average read-count per nucleotide was calculated for IP and input samples. For regions where the IP sample had at least the average read-count, a ratio of IP-input (in log2 scale) was calculated. If the read count in the input was below the average read-count (in the input sample) it was set to the average. All ratio values were then adjusted by reducing each value with the average read-count in IP minus the average read-count in input. This linear adjustment was to normalize for differences in sequencing depth of IP and input. Ratio values every 10bp were extracted across the genome.
Ratio values every 10bp were extracted across the genome, median smoothed using a window size of 500bp and windows with fewer than 25 data points were discarded.
Genome_build: Drosophila melanogaster reference sequence: release 5. Drosophila simulans reference sequence: release 2.
Supplementary_files_format_and_content: BED files with ratio IP/input

organism: Drosophila simulans

source_name: salivary glands from 3rd instar larvae

growth_protocol: larvae were grown at 25°C in potato mash

extract_protocol:
We used 125 salivary glands for each sample. The glands were dissected in PBS and directly transferred to 2% formaldehyde in PBS with 0.1% Triton X-100 for 1–2 min for fixation. The glands were then washed in PBS and glycine was added to a final concentration of 0.125 M. The glands were then washed once in PBS, 1 mM PMSF, protease inhibitor cocktail (Roche) followed by two washes in TBS, 1 mM PMSF, and protease inhibitor cocktail. The samples were homogenized in 250 μl lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1]). Approximately 60 μl glass beads were added prior to sonication for 2 × 10 sec at output level 1, 2 × 10 sec at output level 2, 2 × 10 sec at output level 3 and finally 2 × 10 s at output level 4 (Misonix XL2020, microtip). The samples were cleared by centrifuging for 10 min at 16,000 g. 150 μl of cell lysate was diluted by a factor of ten in ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.0], 167 mM NaCl), and protein inhibitors were added. The diluted lysate was precleared by incubation with 30 μl (60 μl for salivary glands) of Dynabeads conjugated to Protein A (Dynal) and preblocked by equilibration in 150 μl ChIP buffer containing 12 μg (24 μg for salivary glands) sonicated herring sperm DNA. The cleared lysates were then incubated with 3 μl anti-MSL1 , 2 μl anti-MSL2, or 3 μl anti-MOF (from Mitzi Kuroda, Harvard Medical School) antibodies overnight at 4 °C. The antibody complexes were precipitated by incubation with DNA-blocked Protein A Dynabeads for 1 h at 4 °C. The beads were washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl [pH 8.0], 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl [pH 8.0], 500 mM NaCl), once with LiCl-containing buffer (250 mM LiCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate), and twice with TE Buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA). The protein/DNA complexes were eluted from the antibodies by incubating them for 2 × 15 min at room temperature in 250 μl Elution buffer (1% SDS, 0.1 M NaHCO3) with rotation. NaCl was added to a final concentration of 200 mM, and protein/DNA crosslinks were reversed by heating at 65 °C for 4 h. A total of 10 μl of 0.5 M EDTA, 20 μl of 1M Tris-HCl [pH 6.5], and 1 μl of 20 mg/ml proteinase K were added before an additional incubation at 45 °C for 1 h. The DNA was recovered by phenol/chloroform extraction followed by ethanol precipitation. The immunoprecipitated DNA was then dissolved in 24 μl water.
SOLiD (TM) Library Preparation - Uppsala Genome Center ; Size selection (100-150 bp + adapters 90bp < 250bp)

value: wild type (w[501])

value: MOF

value: salivary gland


title: Dsim_MSL2

description: ChIP-seq


title: Dsim_MSL1

description: ChIP-seq


title: Dsim_input

description: ChIP-seq


title: st10.5 uninjected control

city: Irvine

first: William

last: Chiu

address: Room 4410 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California, Irvine

description: processed data file: st10.5_Foxh1_MO_gene_exp_diff.txt

data_processing:
Raw RNA-seq reads from Illumina sequencing were mapped to the most recent Xenopus tropicalis genome assemblyusing TopHat (v. 1.3.3) (Trapnell et al. 2009), with a parameter “-G <Xentr7_2_Stable.gff3>”.
The differential expression of genes in control versus perturbed samples were calculated using Cuffdiff (v. 1.3.0) (Roberts et al. 2011) with default settings.
Genome_build: Xenopus tropicalis genome build v 7.1
Supplementary_files_format_and_content: tab-delimited text file containing FPKM values of all annotated gene models and the fold change of each gene in perturbed versus control embryos

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were cultured in 1/9X MMR at 25°C until the indicated stage.

extract_protocol:
Total RNAs were extracted from ~25-30 control and experimental early gastrula embryos using the acid guanidinium thiocyanate phenol chloroform method (Chomczynski and Sacchi 1987), followed by selective precipitation of RNA using 2.5M LiCl.
Libraries were prepared using illumina TruSeq™ RNA Kit

treatment_protocol: Embryos were treated with SB431542 (100μM) at 4-cell stage until stage 10.5 or microinjected with Foxh1 MO (22.5ng) at 1-2 cell stage and cultured until stage 10.5

value: Nigerian

tag: developmental stage

value: mid-gastrula stage (st10.5)

value: none (control)


title: C2b Scl/TAL1 ChIP-Seq

city: Oxford

first: Richard

middle: J

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

data_processing:
Reads were aligned to the repeat masked hg18 reference genome (UCSC Genome Browser repeatmasker track) using bowtie (version 0.12.3) with the –m reporting option set to 2.
Peak detection was performed as follows. SeqMonk, using the “contig probe generator” option (230 bp contig of overlapping reads with a depth cutoff of 3) was used to call peaks. Peaks in C1 and C2 were then quantified by normalising the number of reads in each peak for the total number of reads detected within peaks. Of the 4538 total peaks initially identified, only peaks containing a minimum of 32 reads in either C1b or C2b were retained. These peaks were then overlapped and annotated with the Encode generated file (ftp://hgdownload.cse.ucsc.edu/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeMapability/wgEncodeDukeRegionsExcluded.bed6.gz), which contains regions in the genome which strongly overreact in high-throughput sequencing experiments due to large copy number differences between the real genome and the genome build, and therefore normalize poorly. After removal of these regions, 2936 peaks remained.
Genome_build: hg18
Supplementary_files_format_and_content: tab delimited table of read count values for called peaks in each sample normalised to the largest data store value (sample C1b) . Differential peaks are annotated in column 4 as are the differntial peaks validated by QPCR, Previously reported targets of Scl/Ta1 are annotated in column 1.

source_name: Erythroid cells

growth_protocol: Two-phase culture system as from Pope SH et al Two-phase liquid culture system models normal human adult erythropoiesis at the molecular level. Eur J Haematol. 2000;64:292-303. Cells were harvested at day 10 of the second phase.

extract_protocol:
ChIPs were performed according to the Millipore ChIP protocol. 5x10^6 cells were fixed with 1% formaldehyde for 10 minutes at RT and chromatin was sonicated to a size <500 bp. Lysates were clarified from sonicated nuclei. Immunoprecipitations were performed, after an overnight incubation with the Scl/TAL1 antibody, with protein A agarose (Millipore). Immunoprecipitated DNA were purified by phenol and chloroform extraction followed by ethanol precipitation.
ChIP-DNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Erythroid cells

tag: culture

value: 10 days

tag: chip antibody

value: Scl/TAL1 (gifted by C. Porcher). Porcher et al Specification of hematopoietic and vascular development by the bHLH transcription factor SCL without direct DNA binding. Development. 1999;126:4603-4615.

tag: individual


title: C1a Scl/TAL1 ChIP-Seq

value: Two-phase culture system as from Pope SH et al Two-phase liquid culture system models normal human adult erythropoiesis at the molecular level. Eur J Haematol. 2000;64:292-303

tag: time


title: st10.5 SB431542 treated

description: processed data file: st10.5_SB431542_gene_exp_diff.txt

tag: strain

value: SB431542 in DMSO/EtOH treatment at 4-cell stage


title: C2a Scl/TAL1 ChIP-Seq


title: C1b Scl/TAL1 ChIP-Seq


title: st10.5 solvent-only control

value: DMSO/EtOH only solvent treatment


title: st10.5 FoxH1 MO

value: 22.5ng Foxh1 MO microinjected at 1-2 cell stage


title: st10.5_input

data_processing:
Raw ChIP-seq reads from the replicates were pooled and mapped to an indexed Xenopus tropicalis genome using Bowtie (v. 0.12.9) (Langmead et al. 2009), only uniquely mapped reads were retained, i.e. parameters: -m 1
MACS (v. 2.0.10) (Zhang et al. 2008) and SISSRs (v. 1.4) (Jothi et al. 2008) were used for peak calling. Effective genome size is 1.16e+09. MACS was run with default setting, Sissrs was run with parameter -a
Peaks were assigned to the nearest genes, using BEDTools (v 2.16.2) (Quinlan and Hall 2010), based on the following criteria:  peak summits need to lie within 10 kb upstream of the 5’ end, within the gene body (5’ UTRs, exons, introns, and 3’UTRs), or 10 kb downstream of the 3’ end of the gene.
Genome_build: Xenopus tropicalis genome build v 7.1
Supplementary_files_format_and_content: bed format of peaks only called by both MACS and Sissrs

extract_protocol:
The fixed embryos were homogenized with an Eppendorf tube pestle and microfuged at 14,000rpm, 4°C for 15 minutes. The pellets, which contain chromatin, were re-suspended in 750ul RIPA buffer and sonicated on ice using a Branson Digital Sonifier 450 (18% power output, 20 sec per pulse, 10 pulses) resulting in DNA fragmentation with a maximum between 200-500bp long. The resulting samples were microfuged at 4°C and 14,000 rpm for 20 minutes to remove insoluble cellular debris. Supernatant containing fragmented chromatin was “pre-cleared” by incubating with 20μl Protein A-coated Dynabeads (Invitrogen) for 2 hour at 4°C. 50 embryo equivalent (eeq) volume of the chromatin supernatant was frozen for use as “input control”. Antibodies were pre-bound to 20μl of Protein A Dynabeads (per batch of 200 embryos) by incubating at 4°C for 30 min. Sonicated chromatin fragments were then added to antibody-bound Dynabeads and incubated overnight at 4°C on an end-over-end rotator. The next day, supernatants were discarded, the recovered beads were washed once with ice-cold ChIP wash solution I (50mM HEPES-KOH pH7.5, 2mM EDTA, 150mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100, 1mM DTT, and 0.4mM PMSF), ChIP wash solution II (50mM HEPES-KOH pH7.5, 2mM EDTA, 500mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100, 1mM DTT, and 0.4mM PMSF), and ChIP wash solution III (0.25 M LiCl, 1 mM EDTA, 10 mM Tris-HCl pH 8.0, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM DTT, and 0.4 mM PMSF), and finally ice-cold TE (10mM Tris, 1mM EDTA, 1 mM DTT, and 0.4 mM PMSF). The DNA was then eluted with TE buffer containing 1% SDS, and reverse-crosslinked at 65°C for 6 hours to overnight. Frozen sonicated input control chromatin frozen was diluted with elution buffer (3-fold) and also incubated at 65°C. On the following day the samples were treated with RNAse A (0.2μg/μl) for 2hr at 37°C, followed by Proteinase K (0.2μg/μl) for 2hr at 55°C, followed by phenol/chloroform extraction and ethanol precipitation. DNA pellets were resuspended in Qiagen EB solution. For ChIP-qPCR analyses on enriched chromatin fragments, immunoprecipitated DNA was amplified using specific primers to detect enrichment in the denoted genomic regions. Results were normalized against input DNA.
Libraries were prepared using Bioo Scientific NEXTflex™ ChIP-seq Kit (Cat# 5143-01)

treatment_protocol: Two thousand embryos were cultured until early gastrula (stage 10.5). Embryos were crosslinked in batches of 200 embryos with 1ml 1% formaldehyde in 1/9XMMR at room temperature for 45 minutes with gentle rocking. Crosslinking reactions were neutralized by removal of the formaldehyde solution and incubation in 1ml 0.125M glycine for 5 minutes at room temperature. Processed embryos were washed twice with ice-cold RIPA buffer (50 mM Tris-HCl pH7.4, 150mM NaCl, 1mM EDTA, 0.25% sodium deoxycholate, 1% NP40, 0.1% SDS, 0.5 mM DTT, and Roche cOmplete protease inhibitor cocktail). The samples can be flash-frozen in liquid nitrogen and stored at -80°C


title: 1143T

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

description: snap-frozen tissue

data_processing:
adapter cutting - cutadapt, obtained sequences with the length of 15-28 nucleotides were subject to further analysis as potential miRNAs
alignment to reference sequences - bowtie
sam to bam format compression - samtools
reads counting - miRs: a number of all reads mapped to each reference sequence,R/Bioconductor ShortRead library
reads counting - isomiRs: a number of each of unique reads mapped to each reference sequence,R/Bioconductor ShortRead library
normalization - Reads Per Million (RPM)
Genome_build: reference sequences were prepared by identifying the sequences of human mature miRNAs, together with 5 flanking nucleotides, within the hairpins deposited in miRBase, version 19
Supplementary_files_format_and_content: tab separated text file with RPM normalized miRNA abundance in 48 samples,  tab separated text file with RPM normalized miRNA isoform counts in 48 samples

source_name: Hepatocellular carcinoma liver cells

extract_protocol:
Total RNA was extracted with TRIzol solution (Invitrogen),and the integrity of RNA was assessed using Agilent BioAnalyzer2100 (Agilent).
Small RNA fraction (with length not exceeding 50 nt) was subjected to hybridization and ligation with Adaptor Mix (NewEngland Biolabs). Subsequently, RNAs were reverse transcribed and sequenced using whole-transcriptome sequencing on the IlluminaHiSeq2000 platform.

tag: type of liver tissue

value: Hepatocellular carcinoma tumor

tag: cirrhosis

value: no

tag: hbv/hcv infection

value: F


title: 1114T

description: snap-frozen tissue

value: yes

value: M


title: miRi02

description:
miRNA
Processed data file column miRi02

tag: tissue

value: primary colon adenocarcinoma

tag: tnm-stage

value: TNM-stage III

tag: age at surgery (yr)

value: female

value: metachronous metastasis


title: 1099N

description: snap-frozen tissue

source_name: Unaffected liver cells tissue adjacent to tumor

value: Unaffected tissue adjacent to tumor


title: 1099T

description: snap-frozen tissue


title: st10.5_Foxh1_ChIP_rep1

description: processed data file: st_10.5_Foxh1_peaks_MACS_SISSRs_overlap.txt

value: Nigerian

value: mid-gastrula stage (st10.5)

value: rabbit anti-Foxh1 antibody

tag: chip antibody vendor

value: custom-made


title: X+P MEF Input DNA Rep2

city: Boston

first: Jeannie

last: Lee

address: 185 Cambridge St, CPZN6

department: Department of Molecular Biology

institute: Massachusetts General Hospital

description: Input DNA Sequencing in  Xist transgenic (X+P) male cells

data_processing:
Basecalls performed using OLB 1.8
Sequences were aligned to the mm9 genome using bowtie 0.12.7, duplicates were removed
Aligned and filtered sequences were used to compute input normalized read densities using the SPP software (bw files)
Genome_build: mm9

source_name: SV40T transformed fibroblasts

growth_protocol: MEFs were maintained in DMEM supplemented with 10% serum. Undifferentiated male J1 and female EL16.7 ES cells were trypsinized to a single cell suspension and MEFs were panned out. 3 X106 ES cells were transferred to a low binding 15cm plate in media not supplemented with LIF. On day 4, embryoid bodies were plated on gelatinized tissue culture plates and harvested at Day 7 for ChIP Seq.

extract_protocol:
Lysates were sonicated in a covaris S2, precleared with protein G agarose and protein-DNA complexes were precipitated using specific antibodies.
Paired end ChIP-sequencing library preparation kit (E6240S) and Illumina multiplexing oligos (E7335S) were purchased from New England Biolabs. Libraries were quantified on a Bioanalyzer using the Agilent high sensitivity DNA kit (Agilent Technologies Cat. No. 5067-4627) and by qPCR using the KAPA library quantification kit (KAPA Biosystems Inc Cat. No. KK4824). Pooled samples were sequenced using Illumina HiSeq 2000 resulting in approximately 25-50 million of 50 bp paired-end reads per sample.

treatment_protocol: Cells were trypsinized and fixed with 1% formaldehyde for 5 minutes at room temperature and quenched by addition of glycine to 0.125M final concentration. Chromatin from 1X 107 cells was sheared in a Covaris S2 and 1/4th of the chromatin (equivalent to 2.5 X 106 cells) was used per ChIP. Samples were incubated with 2μg of specific antibodies overnight. Blocked protein A agarose or dynabeads were added for 2-3 hours and antibody-antigen complexes were washed in buffer containing 250mM NaCl. Complexes were eluted, crosslinks reversed and phenol chloroform extraction was performed using phase lock heavy gels. The eulates were ethanol precipitated and processed for real time PCR analysis or library preparation.

tag: Sex

value: Male

value: SV40T transformed fibroblasts

tag: antibody

value: Xist transgenic (X+P) cells


title: 1114N

description: snap-frozen tissue

tag: gender

tag: age


title: shATRX X+P MEF EZH2 ChIP-seq Rep2

description: Enhancer of Zeste 2 (EZH2) ChIP Sequencing in ATRX Knock down (shATRX) Xist transgenic (X+P) male cells

tag: cell type

value: ATRX Knock down (shATRX) Xist transgenic (X+P) cells


title: miRi03

description:
miRNA
Processed data file column miRi03

value: male

tag: metastasis status


title: shATRX X+P MEF H3K27me3 ChIP-seq Rep2

description: Histone H3 Lysine 27 trimethyl (H3K27me3) ChIP Sequencing in ATRX Knock down (shATRX) Xist transgenic (X+P) male cells


title: 1096N

description: snap-frozen tissue

value: F


title: 1096T

description: snap-frozen tissue

value: Hepatocellular carcinoma tumor

value: yes


title: 1097N

description: snap-frozen tissue

value: no

value: M


title: 1097T

description: snap-frozen tissue


title: 1086T

description: snap-frozen tissue


title: shATRX X+P MEF H3K27me3 ChIP-seq Rep1


title: shATRX X+P MEF Input DNA Rep2

description: Input DNA Sequencing in ATRX Knock down (shATRX) Xist transgenic (X+P) male cells


title: 1041T

description: snap-frozen tissue


title: 1039T

description: snap-frozen tissue


title: shATRX X+P MEF Input DNA Rep1

value: IATRX Knock down (shATRX) Xist transgenic (X+P) cells


title: 1039N

description: snap-frozen tissue


title: shATRX X+P MEF EZH2 ChIP-seq Rep1


title: 1038T

description: snap-frozen tissue


title: X+P MEF EZH2 ChIP-seq Rep2

description: Enhancer of Zeste 2 (EZH2) ChIP Sequencing in  Xist transgenic (X+P) male cells


title: 1143N

description: snap-frozen tissue


title: 1037N

description: snap-frozen tissue


title: X+P MEF H3K27me3 ChIP-seq Rep1

description: Histone H3 Lysine 27 trimethyl (H3K27me3) ChIP Sequencing in  Xist transgenic (X+P) male cells


title: 1032T

description: snap-frozen tissue


title: 1041N

description: snap-frozen tissue


title: X+P MEF H3K27me3 ChIP-seq Rep2


title: 1037T

description: snap-frozen tissue


title: 1034T

description: snap-frozen tissue


title: X+P MEF EZH2 ChIP-seq Rep1


title: 1034N

description: snap-frozen tissue


title: 1038N

description: snap-frozen tissue


title: 1086N

description: snap-frozen tissue


title: 1025N

description: snap-frozen tissue


title: MEF ATRX ChIP-seq Rep2

description: ATRX ChIP Sequencing in transformed female mouse embryonic fibroblasts (MEF)

value: Female

value: 129S1/CastEiJ x 129S1

value: ATRX

value: transformed embryonic fibroblasts (MEF)


title: MEF Input DNA Rep2

description: Input DNA Sequencing in transformed female mouse embryonic fibroblasts (MEF)


title: 1032N

description: snap-frozen tissue

value: Unaffected tissue adjacent to tumor


title: 1025T

description: snap-frozen tissue


title: 1023N

description: snap-frozen tissue


title: MEF Input DNA Rep1


title: 1023T

description: snap-frozen tissue


title: 1022T

description: snap-frozen tissue


title: 1016T

description: snap-frozen tissue


title: 1016N

description: snap-frozen tissue


title: 1022N

description: snap-frozen tissue


title: 1018N

description: snap-frozen tissue


title: 1018T

description: snap-frozen tissue


title: MEF ATRX ChIP-seq Rep1


title: X+P MEF Input DNA Rep1


title: 1015T

description: snap-frozen tissue


title: 1014T

description: snap-frozen tissue


title: 1012T

description: snap-frozen tissue


title: 1013T

description: snap-frozen tissue


title: 1015N

description: snap-frozen tissue


title: ES cell d7 Input DNA Rep1

description: Input DNA Sequencing in Day 7 differentiated (D7) female embryonic stem cells

source_name: Day 7 differentiated mouse embryonic stem cells

value: F2:129S1/CastEiJ x 129S1


title: ES cell d7 ATRX ChIP-seq Rep2

description: ATRX ChIP Sequencing in Day 7 differentiated (D7) female embryonic stem cells

value: Day 7 differentiated mouse embryonic stem cells


title: ES cell d7 ATRX ChIP-seq Rep1


title: 1013N

description: snap-frozen tissue


title: ES cell d0 Input DNA Rep2

description: Input DNA Sequencing in undifferentiated (D0) female embryonic stem cells

source_name: Undifferentiated mouse embryonic stem cells


title: ES cell d0 ATRX ChIP-seq Rep2

description: ATRX ChIP Sequencing in undifferentiated (D0) female embryonic stem cells

value: Undifferentiated mouse embryonic stem cells


title: 1012N

description: snap-frozen tissue


title: ES cell d7 Input DNA Rep2


title: 1010N

description: snap-frozen tissue


title: 1010T

description: snap-frozen tissue


title: 1009T

description: snap-frozen tissue


title: 1009N

description: snap-frozen tissue


title: ES cell d0 ATRX ChIP-seq Rep1


title: ES cell d0 Input DNA Rep1


title: ATRX KD MEF Input DNA

description: Input DNA Sequencing in ATRX knockdown transformed female mouse embryonic fibroblasts

value: SV40T transformed fibroblasts

value: ATRX knockdown transformed embryonic fibroblasts


title: 1001T

description: snap-frozen tissue


title: ATRX KD MEF ATRX ChIP-Seq

description: ATRX ChIP Sequencing in ATRX knockdown transformed female mouse embryonic fibroblasts


title: Input_H3K4me2_Bizine_1

city: Guangzhou

first: Xin

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

country: China

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Paired-end sequencing data were aligned to the reference human genome (hg19) using BWA with default parameters. After alignment, duplicate reads were removed and only uniquely aligned reads were kept for further analysis
MACS2 were used for peak calling with default parameters.
Differential peaks between samples with two biological replicates were identified by diffReps. Ensemble human genome annotations were used to identify the human genes around identified peak regions. A gene is defined to be around a peak region if the closest distance between its Transcription Start Site (TSS) and the peak region is less than 2000bp.
Genome_build: hg19

source_name: LNCaP cells

growth_protocol: LNCaP cells were maintained in RPMI 1640 + GlutaMAX (Invitrogen 61870-036) supplemented with 10% fetal bovine serum (FBS, Gibco 10437-028) and 1 unit mL-1 penicillin, 1 μg mL-1 streptomycin (Gibco 15140-122). Cells were grown at 37 °C in 5%/95% CO2/air.

extract_protocol:
Cells were then cross-linked with 1% formaldehyde for 10 min at 37 °C. Cells were then placed on ice and washed with ice cold PBS (2 x 10 mL), scraped and pelleted. Pellets were then resuspended in PIPES buffer (5 mM PIPES (pH 8.0), 85 mM KCl, 0.5% NP-40, 1x cOmplete, EDTA-free, Protease Inhibitor Cocktail Tablets (Roche)), lysed in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, 1x cOmplete, EDTA-free, Protease Inhibitor Cocktail Tablets (Roche)), and sonicated to shear cross-linked DNA. Samples were kept in an ice bath at all times. Nucleic acid concentration was then measured using a Nanodrop (Thermo Scientific). The nucleic acid (20-100 μg) was then resuspended in 450-1,000 μL ChIP dilution buffer (0.01% SDS, 1.1% Triton-X 100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, 1x cOmplete, EDTA-free, Protease Inhibitor Cocktail Tablets (Roche)), and pre-cleared by adding 30 μL Protein A Dynabeads (Invitrogen) and rotated for 30 minutes at 4°C. Samples were then incubated overnight at 4 °C with 5 μg of polyclonal rabbit H3K4Me2 (milipore 07-030) (a no antibody control sample was included). 65 μL Dynabeads were then added to the samples and rotated for 2 h at 4°C. Dynabeads were then washed 2x with a low salt wash (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.1, 150 mM NaCl); 1x with LiCl wash (0.25 M LiCl, 0.5% NP-40, 0.5% Na Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1); and 2x with TE pH 8.0. Elution buffer was then added to the beads (1% SDS, 0.1 M NaHCO3) and samples were vortexed and rotated at RT for 15 minutes and sample transferred to a new tube. This step was repeated 2x. Cross-linking was reversed by the addition of 20 μL 5 M NaCl and heating at 65°C for 4 h. 10 mM EDTA, 40 mM Tris-HCl pH 6.5, and 40 μg Proteinase K (Thermo Scientific #EO0491) were then added and samples were incubated for 1 h at 45 °C. 500 μL phenol:chloroform was then added to the samples and they were rotated overnight at 4°C. Samples were then spun and the top layer (aqueous) was placed in a new tube. An equal volume of chloroform was added and vortexed and spun and the bottom layer discarded again. 50 μg mL-1 of GlycoBlue (Life Technologies AM9515), 0.5 M NaOAc pH 5.2, and 2 volumes of 100% ethanol was added and samples were placed on ice for 15 minutes. Samples were then spun down and pellet was washed with 1 volume 70% EtOH and let dry. The pellets were then resuspended in TE and DNA concentrations were quantified by Qubit assay HS kit (Invitrogen Q32851).
Libraries were prepared from 10-20 ng of IP ChIP DNA and 100 ng of input DNA according to Illumina’s instructions along with the ChIP-seq DNA Sample Prep Kit (IP-102-1001). Briefly, samples were checked for quality and concentration from 150-250 bp on a bioanalyzer. DNA was end-repaired using Klenow polymerase in 58 μL of reaction buffer. For IP DNA, Klenow was diluted 1:5. Samples were incubated at 20°C for 30 minutes and subsequently purified on QIAquick PCR purification columns. A-tails were then added to the DNA with Klenow and dATP in NEB buffer 2 at 37°C for 30 minutes and cleaned with Qiagen MiniElute PCR purification columns. Sequencing adapters were then ligated onto the DNA for 15 minutes at room temperature followed by cleaning with MiniElute columns. Samples were then run on 2% agarose gels and DNA from 216-366 bp (DNA plus adapters) were cut from the gel and purified with a Qiagen QIAquickGel Extraction kit. Concentrations were then checked on a bioanalyzer and 8 ng were PCR amplified with Phusion polymerase (Fisher) for 15 cycles (10 sec 98°C, 30 sec 65°C, 30 sec 72°C) followed by 5 minutes at 72°C. Samples were then cleaned with Ampure kits (Illumina) and washed with 80% ethanol. DNA samples were resuspended at the end of the cleanup into 17.5 μL buffer EB (Qiagen) and subjected to next generation sequencing on Illumina HiSeq platform according to manufacturers instructions.

treatment_protocol: LNCaP cells were seeded in 2, 150 x 25 mm tissue culture dishes (Corning 430599) per condition. Cells were grown to ~70% confluency, and after washing with phosphate-buffered saline (2 x 10 mL) (PBS, Gibco 10010-023), the cells were treated with either vehicle (DMSO) or 10 μM 12d (bizine) (>97% purity as determined by NMR)  and grown in serum-free media for 48 h.

tag: passages


title: 1014N

description: snap-frozen tissue


title: 1001N

description: snap-frozen tissue


title: Input_H3K4me2_Bizine_2


title: H3K4me2_Bizine_1


title: H3K4me2_Bizine_2


title: Input_H3K4me2_DMSO_1


title: H3K4me2_DMSO_1


title: H3K4me2_DMSO_2


title: Control_Ab_mLama4_pos_rep3

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 50bpX25bp pair-end! 10 sequencing. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to mm9 genome using TopHat with following options -G mm9.mrna.10.31.gtf --prefilter-multihits --segment-length 20 --max-multihits 15. Geneexpression was obtained using ESAT software tool(http://garberlab.umassmed.edu/software/esat/) focused on analysis of 3’end targetedRNA-Seq. The following parameters were used: -task "score3P" –normalizedOutput -window 1000 -maxExtension 3000 -maxIntoGene 2000 -stranded –collapseIsoforms.
Genome_build: mm9
Supplementary_files_format_and_content: comma delimited file that includes normalized count data for each sample and tab delimited file with barcode annotations

source_name: tumor infiltrating lymhpocytes

extract_protocol:
For sorting of mLama4-specific cells, tumour-infiltrating cells were enriched for CD45+ cells using CD45 cell purification magnetic beads (Miltenyi Biotec). CD45 enriched cells were then sorted gating for PI- CD3ε+ CD8α+ mLama4-tetramer-PE+ or PI- CD3ε+ CD8α+ mLama4-tetramer-PE- cells. Sorting was performed on a BD FACSAria II (BD Biosciences). Sorted cells were pelleted and processed for RNA analysis. All flow cytometry was performed on the FACSCalibur (BD Biosciences) or LSR Fortessa (BD Biosciences) and analysed using FlowJo software (TreeStar).
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen). For cDNA synthesis, we used custom oligo-dT primer with a barcode and adapter-linker sequence (CCTACACGACGCTCTTCCGATCT—XXXXXXXX-T15). After first strand synthesis samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded using consecutive acid-alkali treatment. Then, second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (New EnglandBiolabs, Ipswich, MA) and after SPRI clean-up, mixture was PCR enriched 14 cycles andSPRI purified to yield final strand specific 3'end RNA-seq libraries
3'end DGE

value: tumor infiltrating lymhpocytes

tag: treatment

value: Control Ab


title: Input_H3K4me2_DMSO_2


title: Control_Ab_mLama4_pos_rep1


title: Control_Ab_mLama4_pos_rep2


title: Control_Ab_mLama4_neg_rep3


title: aPD1_plus_aCTLA4_mLama4_pos_rep3

value: aPD1 plus aCTLA4


title: Control_Ab_mLama4_neg_rep2


title: Control_Ab_mLama4_neg_rep1


title: G2_phase_synchronized_RNA-seq biological replicate #2

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

data_processing:
RNA sequences (90 bp) were quality assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html)
RNA sequence analysis was performed using the cufflinks suite  and -T operator
Genome_build: ASM294v2

organism: Schizosaccharomyces pombe

source_name: cdc25-22 (G2 phase) synchronized Schizosaccharomyces pombe

growth_protocol: Schizosaccharomyces pombe strains were recovered from -80°C on YES (2% agar) plates (26°C, 4 days). YES medium (12 ml) starter cultures were inoculated and incubated (26°C, 200 rpm) until the OD595 measured ~0.8 (~24 h).

extract_protocol: For RNA extraction, cells were harvested from 12 ml of each synchronized cell culture prior to cross-linking (4,000 rpm, 2 min, RT), washed with 5 ml of AE buffer (50 mM Sodium Acetate, 10 mM EDTA, pH 5.3), and suspended in AE buffer (400 μl). Cell suspensions were transferred to tubes containing an equal volume of phenol/chloroform/isoamyl alcohol (24/24/1 Ambion) and 400 μl of acid washed glass beads (Invitrogen). Tubes were transferred to a chilled block (-20°C) in a Geno/Grinder (SPEX sample prep 2010) and the cells were lysed (1,750 rpm, 8 x 30 sec on 60 sec off). Lysis was completed by freeze (-80oC, ~15 min), thaw before centrifugation (14,500 rpm, 5 min, 4°C). The aqueous phase was extracted three times with an equal volume of phenol/chloroform/isoamyl alcohol. RNA was isolated by precipitation with 1/10th volume ammonium acetate (5 M) and 2 volumes of 100% ethanol at -80°C (>30 min/over-night) before centrifugation (14,500 rpm, 10 min, 4°C). RNA was washed with 70% ethanol (350 μl; 14,500 rpm, 5 min, 4°C) and air dried (37°C, ~15 min). RNA pellets were suspended in RNASecure (80 μl; Ambion) and dissolved by heating (60°C, 10 min).

treatment_protocol: Synchronization cultures (125 ml EMM2, in baffled flasks) were inoculated with starter culture to an OD595 = ~0.05 and incubated (26°C, 120 rpm). Cultures were grown for four generations (OD595 ~0.8) before synchronization was induced by the addition of pre-warmed EMM2 medium (125 ml, 46°C), instantly rising the temperature of the culture to the restrictive temperature (36°C). Cultures were incubated in a hot water bath (36°C, 140 rpm, for 4 h) to complete synchronization.

tag: cell cycle

value: G2 phase


title: G2_phase_synchronized_RNA-seq biological replicate #1

tag: strain


title: aPD1_plus_aCTLA4_mLama4_pos_rep2


title: M_phase_synchronized_RNA-seq biological replicate #1

source_name: nuc2-663 (M phase) synchronized Schizosaccharomyces pombe

value: M phase


title: M_phase_synchronized_RNA-seq biological replicate #2


title: aPD1_plus_aCTLA4_mLama4_pos_rep1


title: aPD1_plus_aCTLA4_mLama4_neg_rep2


title: aPD1_plus_aCTLA4_mLama4_neg_rep1


title: aPD1_mLama4_pos_rep2


title: G1_phase_synchronized_RNA-seq biological replicate #1

source_name: cdc10-129 (G1 phase) synchronized Schizosaccharomyces pombe

value: G1 phase


title: aPD1_mLama4_neg_rep3