title: 24_miRNA

status: Public on Jul 07 2013

city: Hangzhou

first: Xiangbin

last: Xu

address: Xiasha xuelin street 16

institute: Hangzhou Normal University

description: processed data file: Table S4.xls

data_processing:
The small RNA sequences were processed using Illumina’s Genome Analyzer Pipeline software to filter out the 5’ and 3’ adapter sequences, and low quantity reads, and then subjected to a series of data filtration steps to obtain mappable sequences using ACGT101-miR v4.2 (LC Sciences, TX, USA). After removed the mRNA and Rfam (rRNA, tRNA, snRNA, snoRNA and repeat sequence), all the trimmed sequences between 15 and 32 bp in length were mapped to miRNA sequences from the miRNA database, miRbase 19.0 (http:// www.mirbase.org/).
To identify potential miRNA precursor sequences, all identified strawberry fruit mature miRNA sequences were BLASTed against the strawberry genome sequences which downloaded from database (http://www.rosaceae.org/). Secondary structure prediction of miRNA precursor was performed by UNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). In addition, the rest unmapped small RNA sequences were also BLASTed against the strawberry genome sequences and the secondary structure were predicted as above. The non-coding sequences which could form a perfect stem-loop structure and meet the standard of miRNAs prediction [25] were regarded as novel miRNA candidates.
A Public software package, CleaveLand3.0 was used for analyzing the degradome sequencing data
Genome_build: fvesca_v1.0_genemark_hybrid.fna.gz at: http://www.rosaceae.org/projects/strawberry_genome/v1.0/genes/
Supplementary_files_format_and_content: details on README.txt

organism: Fragaria x ananassa

source_name: strawberry fruit_24h storage

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions. Small RNA libraries were generated from the two samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.

treatment_protocol: Strawberry (Fragaria ananassa L. cv. Zhangji) fruits were harvested at commercial maturity and sorted based on size without physical injuries or infections. Then  put in trays with plastic bag to maintain a relative humidity (about 85%), and stored at 20 °C for 0, 24 h.

tag: species

value: Fragaria ananassa L. cv. Zhangji

tag: development

value: postharvest

value: fruit

tag: sample group

value: 24 h storage


title: targets

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

source_name: strawberry fruit

tag: tissue

value: 0-24 h storage


title: Normal Brain 2

city: Philadelphia

first: Paul

last: Ryvkin

state: PA

address: 423 Guardian Dr, 1404 Blockley Hall

department: Pathology

country: USA

institute: University of Pennsylvania

description: small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence using cutadapt v0.9 with options "-e 0.06 -O 6 -m 14 -n 2" and untrimmed reads were discarded.
Reads were mapped to the genome (hg19) using bowtie with options "--best --strata -v 2 -k 100" and non-unique mappers were removed. Reads with a mismatch rate > 6% were discarded.
Locus annotations were generated by calling clusters of (only uniquely-mapped) small RNA reads via RSeqTools bgrSegmenter. (minRun=14, maxGap=44, threshold=10). These were then overlapped with UCSC tracks knownGene, rmsk, tRNAs, wgRNA and the Human lincRNA Catalog (stringentSet). Multiple overlapping loci were prioritized as per the file class_pri.txt (lower value is higher priority).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed sequence

organism: Homo sapiens

source_name: Dorsolateral prefrontal cortex

extract_protocol:
RNA was harvested from frozen brain tissue using Trizol reagent.
Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA.

value: brain (dorsolateral prefrontal cortex)

tag: gender

value: female

tag: disease state

value: normal


title: 0_miRNA

description: processed data file: Table S4.xls

source_name: strawberry fruit_0h storage

value: 0 h storage


title: Snyder_ZIP-2_GFP_L4_Input_Rep2

status: Public on Jul 11 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

library_source: genomic

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

molecule: genomic DNA

organism: Caenorhabditis elegans

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

tag: strain

value: OP432(official name :OP432 genotype :unc-119(ed3) III; wgIs432(zip-2::TY1-GFP-3xFLA;unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description :using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZIP-2::EGFP fusion protein is expressed in the correct zip-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZIP-2 transcription factor. made_by :Unknown )

tag: developmental stage

tag: genotype

tag: Sex

value: Hermaphrodite


title: Normal Brain 1

description: small RNA


title: Normal Brain 4

description: small RNA


title: RC_input_DNA

status: Public on Jul 05 2013

city: Dallas

first: Ling

last: Cai

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center at Dallas

description: Input DNA.

data_processing:
The fastq files were generated using CASAVA version 1.7.
4bp barcode was removed from the 40 bp reads.
Reads were aligned to the sacCer1 genome assembly using Bowtie-0.12.5 with parameters -m 1.
Data were processed by CisGenome. 2 sample ChIP analysis was performed using ChIP as the treated sample and Input as the control.
Peaks were called by CisGenome.
Genome_build: sacCer1
Supplementary_files_format_and_content: .bar files were generated from Cisgenome and converted to .wig files.

organism: Saccharomyces cerevisiae

source_name: YMC RC phase cells, input

growth_protocol: Yeast cells from the IFH1-FLAG strain were cultured in a fermentor under low glucose continuous growth conditions as described in Tu, et al. 2005 (PMID 16254148).

extract_protocol: Chromatin was sheared with the Bioruptor and precleared before immunoprecipitation with Flag antibody. The ChIP DNA was purified using MinElute PCR purification kit. ChIP-seq library construction was performed following the protocol at http://bioinfo.mbb.yale.edu/array/Solexa_LibraryPrep_20080229ge.pdf . Briefly, ends were repaired (End-it DNA End Repair Kit, Epicentre, Cat# ER0720), 'A' base was added to the 3' ends (Klenow (3'→5' exo-), NEB, Cat# M0212s), adaptors were ligated (LigaFast, Promega, Cat#M8221 and the adapter mix from Illumina), and PCR was performed (Phusion DNA polymerase, NEB, Cat# F-531 and Illumina primers), followed by size selection.

treatment_protocol: OX and RC phase cells were collected and crosslinked for 15min at room temperature with 1% formaldehyde and quenched with 150mM glycine before being flash frozen.

value: CEN.PK a IFH1-FLAG::Nat

tag: ymc phase

value: RC quiescent phase

tag: chip antibody


title: IFH1_RC_ChIPSeq

description: Chromatin IP against Ifh1-FLAG.

source_name: YMC RC phase cells, Ifh1p ChIP

value: FLAG

tag: antibody vendor

value: Sigma

tag: antibody catalog#


title: pooled total RNA subjected to "long" running  conditions for two dimensional gel electrophoresis

status: Public on Jul 09 2013

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: total pooled RNA was run on a 7.5% acrylamide gel run at 40mA until the xylene cyanol had migrated 31cm, while the second dimension utilized a 20% gel run at 28mA until the xylene cyanol had migrated 68cm

data_processing:
barcode trimming: first three bases at the five prime end of every read were removed
alignment: trimmed reads were uniquely aligned to the S. pombe reference genome using bowtie-0.12.3 with the following parameters: -v0 -m1
peak calling: samtools was used to generate a pileup file from the aligned file from the previous step. In-house perl scripts were used to infer non-zero read regions as "peaks" from the pileup file
peak classification: in-house perl scripts were used to probabilisitcally infer and classify splicing events from peaks, as described in (Supplemental Methods in  www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental)
branch point detection:  in-house perl scripts were used to infer branch points for introns from certain reads, as described in (Supplemental Methods in  www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental)
Genome_build: S. pombe reference genome pombe_040211.fasta, available from www.pombase.org
Supplementary_files_format_and_content: peak raw read counts for previously-annotated introns from the "short" sample
Supplementary_files_format_and_content: peak raw read counts for novel introns from the "short" sample
Supplementary_files_format_and_content: peak raw read counts for exon-skipping events from the "short" and "long" samples
Supplementary_files_format_and_content: branch point sequence, location and read count for introns from the "short" sample

organism: Schizosaccharomyces pombe

source_name: circular RNA portion of total cellular RNA pooled from 41 growth/treatment conditions

growth_protocol: Over 41 different growth and treatment conditions were used for all samples. See Table S1 in www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental

extract_protocol:
Hot phenol extraction of total RNA, followed by pooling of RNA from all 41 growth conditions, then two dimensional acrylamide gel electrophoresis and excision of arc corresponding to circular RNA (see Supplemental Methods in  www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental)
Same as that of Quail et al. Nature Methods 2008 (PMID: 19034268), with slight modifications (see Supplemental Methods in  www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental)


title: Asynchronous GM06990 RNASeq2

city: Charlottesville

first: Stefan

last: Bekiranov

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry & Molecular Genetics

institute: University of Virginia

description:
Poly A selected RNA
CEPH/UTAH PEDIGREE 1331, CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 9; CYP2C9, HUMAN VARIATION PANEL - EUROPEAN CAUCASIAN PANEL OF 8, HUMAN VARIATION PANEL - EUROPEAN CAUCASIAN PANEL OF 16, HUMAN VARIATION PANEL - EUROPEAN CAUCASIAN PANEL OF 24, SNP500 PANE

data_processing:
Illumina Casava1.7 software used for basecalling.
Bubble-seq reads for Samples 1, 2 and 3 were aligned to the hg18 genome assembly using BWA version 0.5.7 and individual enriched read wig files were generated. Reads for the three samples were merged togther and an enriched read wig file was generated for the combined dataset as well. Read depths (RD) were calculated over all EcoRI intervals in the genome - statistically enriched regions, also termed bubbles were determined by fitting to a negative binomial distribution.
RNA-seq reads for Samples 4 and 5 were merged and aligned to the hg18 genome assembly using Bowtie version 0.12.5.0. Parameters used were min-intron-length 30, and a reference transcript annotation file (wgEncodeGencodeManualV3.gtf). RNA-Seq read alignments were converted to SAM format by TopHat version 1.0.13. Cufflinks version 0.8.3 was then used to assemble transcripts from the aligned reads in SAM format, and estimate their relative abundances based on the same reference transcript annotation file.
Genome_build: hg18
Supplementary_files_format_and_content: Wig files of read depths of bubbles, FPKM measurements for genes and transcripts as determined by cufflinks 0.8.3

source_name: lymphoblastoid cell line

growth_protocol: The lymphoblastoid cell line, GM06990, was obtained from Coriell Institute for Medical Research and propagated in RPMI 1640 supplemented with 50ug/ml Gentamicin and 15% serum (Fetal Clone II, Hyclone).  Cells were maintained in culture for no longer than 3 weeks, passaged every 2-3 days and maintained at a cell density of 3-8X105 cells per ml.

extract_protocol: Each RNA-seq library was prepared from poly A+ RNA, which was isolated from 108 asynchronously growing cells.  Each bubble trap library was prepared from DNA that was isolated from 10 preparations of 109 cells (1010 cells per library). The construction and subsequent single-end sequencing of these libraries using an Illumina Gene Analyzer IIx was performed as outlined by the manufacturer.

treatment_protocol: Cells were harvested 36-48h after passage and at a density of 5-6X105 cells / ml.  Total RNA was isolated as outlined (Chomczynski and Sacchi (1987) Anal Biochem 162(1):156-9) followed by poly A+ RNA (Kingston (1992), Current protocols in Molecular Biology. Supplement 21).  Actively initiating replicative DNA (bubbles) was isolated exactly as described (Mesner et al (2009a), Methods Mol. Biol. 521: 121-137; Mesner and Hamlin (2009b), Methods Mol. Biol. 521: 315-328)

tag: cell line

tag: sample type

value: Poly A selected RNA


title: Snyder_DVE-1_GFP_LateEMB_ChIP_Rep2

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

value: OP398(official name :OP398 genotype :unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description :using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by :Unknown )

value: Late Embryo


title: IFH1_OX_ChIPSeq

description: Chromatin IP against Ifh1-FLAG.

source_name: YMC OX phase cells, Ifh1p ChIP

value: OX growth phase


title: OX_input_DNA

description: Input DNA.

source_name: YMC OX phase cells, input


title: NT2 input 2

city: Davis

first: Yoong Wearn

last: Lim

state: CA

address: One Shields Avenue

department: Molecular and Cellular Biology

institute: University of California, Davis

description: gDNA digested with BamHI, NcoI, ApaLI, NheI and PvuII

data_processing:
Library strategy: DRIP-seq
Fastq reads were aligned to hg19 using BWA version 0.6.1
Peak calling was performed using MACS 1.4.2
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated by MACS

source_name: NT2 input 2

extract_protocol:
Genomic DNA was extracted from NT2 cells and was either fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI (DRIP-seq 1) or BamHI, NcoI, ApaLI, NheI and PvuII (DRIP-seq 2). Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrids.
Sequencing library was constructed using standard Illumina protocol.


title: wildtype, 2nd replicate

city: Cambridge

first: Sebastian

last: Hoersch

state: MA

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

description: RNA (via transcriptionally engaged polymerase II)

data_processing:
Library strategy: GRO-Seq
Two independent biological replicates were generated for each strain (N2 (WT) and zfp-1 (ok554)). Sequencing was performed to a length of 50 nucleotides. Since cloned RNA ranged from 16 to 180 nucleotides in length, the sequencing reads were post-processed to eliminate the 3' linker sequence [AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC], if present, so that resulting reads ranged from 16 to 50 nucleotides in length. The reads were then aligned using bwa 0.6.1 to the C. elegans genome (ce6 assembly), and rRNA reads were removed based on genomic location.
After filtering, we obtained 8,484,939 reads from WT (5.039.164 reads from the first replicate and 3,445,775 reads from the second replicate) and 7,539,039 reads from zfp-1 (ok554) (4,765,744 reads from the first replicate and 2,773,315 reads from the second replicate). After ascertaining concordant results with the individual replicate pairs (WT vs. mutant) (data not shown), replicate reads for each WT and mutant were pooled, using  downsampling on the replicate with higher read count to ensure equal representation of either replicate, and the pooled reads were processed together to increase statistical power.
For each annotated C. elegans transcript, the aligned reads were binned based on the annotated transcriptional start site (TSS) and transcriptional termination site (TTS) into 3 regions as follows: 'promoter' (from 600bp upstream of the annotated TSS to 200bp downstream), 'gene body' (from 200bp downstream of the annotated TSS to 200bp upstream of the annotated TTS), and 'gene end' (from 200bp upstream of the annotated TTS to 400bp downstream).
We then calculated region-specific RPKM values (#total reads / (region length (KB) X # mapped reads (M)) for these regions and considered for further analysis only transcripts with RPKM values of > 1 for the 'gene body' (= transcribed genes).
The stalled index was calculated as the log2 ratio of 'promoter' RPKM over 'gene body' RPKM for each gene. Genes with a stalled index more than 1 (i.e. at least twice as many promoter reads as gene body reads) were considered stalled. The average profile in Figure S6B was calculated using Cistrome/Galaxy (Liu et al., 2011) using the CEAS tool (enrichment on chromosome and annotation).
Genome_build: ce6
Supplementary_files_format_and_content: .wig: alignment wiggle files of paired replicates, rescaled to a target of 1 Mio

growth_protocol: Per sample, around 300,000 worms were grown on a large plate and harvested at L3 stage (36 hours after hatching at 20°C).

extract_protocol:
Worms were washed off the plate with cold M9 and washed 3-4 times.  The worm pellet was resuspended in 2ml of cold Nuclear Run-On (NRO) lysis buffer (10mM Tris pH 7.5, 2mM MgCl2, 3mM CaCl2, 0.5% IGEPAL and 10% glycerol), transferred to a steel dounce (on ice) and stroked 20 times.  The worm lysate was centrifuged for 2min at 40g and the supernatant was centrifuged again for 5min at 1000g to pellet the nuclei.  Next, the supernatant was discarded and the nuclei pellet was washed two times with 1ml of cold NRO lysis buffer and one time with 1ml of cold Freezing Buffer (50mM Tris-CL pH 8.3, 40% glycerol, 5mM MgCl2, 0.1 mM EDTA). Nuclei were then resuspended in 100µl of Freezing Buffer and used for the NRO reaction. //  NRO reaction and DNase digestion: 100µl of nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCL, 20 units of SUPERase In, 1% sarkosyl, 500µM ATP, GTP, and Br-UTP, 2μM CTP) and incubated for 5 minutes at 32°C.  The reaction was stopped with 750μl of TRIzol reagent (Invitrogen) and the RNA was extracted following the manufacturer's instructions.  The RNA pellet was resuspended in 85µl water and treated with 5µl of turbo DNase (Ambion) in a total volume of 100µl and incubated at 37°C for 30 minutes.  The RNA was then extracted by phenol:chloroform and precipitated with one volume of isopropanol with 1/10 volume of Sodium Acetate 3M and 10µg of Glycoblue (Ambion).  // Base Hydrolysis of RNA: The hydrolysis of RNA was performed using fragmentation reagent (Ambion) for 15min at 70°C and the product was purified by p-30 RNase free spin column (BioRad), following the manufacturer’s instruction. //  Immunopurification of Br-U RNA and RNA-end repair: The purification of the Br-U RNA and the end repair of the purified Br-U RNA was performed as described in (Core et al., 2008).
Adapter ligation and library preparation:  For the ligation of 5' and 3' adapters to Br-U RNA we used reagents contained in the ScriptMiner™ Small RNA-sequencing kit (Epicentre) and we immunopurified the ligated Br-U RNA product after each ligation with anti-deoxy-BrU beads (Santa Cruz Biotech (sc-32323-AC).  The ligated Br-U RNA was then reverse-transcribed and PCR-amplified with properly-indexed primers for 18 cycles, following the ScriptMiner™ Small RNA-sequencing kit (Epicentre) manufacturer's instructions.  The NRO-cDNA libraries were purified by phenol:chloroform, the DNA was precipitated as above and then ran on a non-denaturing 1XTBE, 8% acrylamide gel and stained with SYBR gold (Invitrogen). DNA fragments ranging in size from 120bp to 300bp was excised from the gel and eluted by incubating in TE + 300mM NaCl overnight with rotation.  The DNA libraries were then extracted, precipitated, and sent for sequencing.

value: whole animal

tag: Stage

tag: age

value: wildtype:Bristol N2


title: zfp-1 mutant, 1st replicate


title: zfp-1 mutant, 2nd replicate


title: Wild Type

status: Public on Jul 08 2013

city: Augusta

first: Wei-Hua

last: Wu

state: GA

address: 1462 Laney Walker Blvd

department: Neurology

institute: IMMAG/MCG/GRU

data_processing:
Sequence reads were aligned using Bowtie 0.12.7.
Nucleosomes were mapped using a TemplateFilter algorithm (Weiner A et al, Genome Research 20: 90-100, 2010)
Nucleosome occupancies were normalized by the total reads numbers, followed by quantile normalization
Genome_build: S. cerevisiae 2003 (Bowtie CYGD default)
Supplementary_files_format_and_content: Text files have the locations and normalized occupancies of nucleosomes

source_name: WT

growth_protocol: Wild type and mutant yeast cells were grow in YPD medium at 30°C and harvested at ~ O.D. 0.5.  Cells were fixed with 1% paraformaldehyde at room temperature for 30 minutes.

extract_protocol:
Crude yeast nuclei was extracted and digested with micrococcal nuclease at 37°C for 10 minutes.  Mononucleosomal DNA was gel purified.
Library was constructed as previously described (Barski A et al, Cell 129: 823-837, 2007)

tag: genotype/variation

value: Wild Type


title: Tcf21MO-45

city: Chapel Hill

first: Panna

last: Tandon

state: NC

address: 220 Fordham Hall

institute: UNC at Chapel Hill

description: Sample 2

data_processing:
Image analysis and base calling was performed by the Sequencing Control Software (SCS) Real Time Analysis (RTA, v.2.6), ran on the Illumina Genome Analyzer control computer at UNC HTSF. Post-processing of the data was performed using the Illumina CASAVA pipeline software (v.1.7) using the default parameters.
Sequenced reads were mapped to a cDNA library from Xenbase (8,879 cDNA sequences annotated as RefSeq sequences, Feb 7th 2012) using default settings on bowtie2 v2.0.0.6 with parameters -x
Samtools v 0.1.18.0 was used to tabulate read counts from aligned reads, indexed from .bam file
Reads were normalized to total read counts and assessed for fold change in experimental Tcf21-depleted gene dataset compared to sibling controls.
Genome_build: Refseq cDNA library from Xenbase (Feb 2012, Taejoon Kwon, University of Austin at Texas, Marcotte lab) was used for read alignments in the absence of an annotated Xenopus laevis genome at the time
Supplementary_files_format_and_content: tab-delimited text files include normalized values for total read counts and fold change

molecule: polyA RNA

organism: Xenopus laevis

growth_protocol: Embryos were injected with MO at fertilization and maintained in 0.1xMBS between 16-23oC until stage 44-45

extract_protocol:
Hearts were dissected from anaethetized embryos, collected into Trizol on ice and flash frozen in liquid nitrogen until processed. Total RNA was harvested using Trizol reagent.1 ug of total RNA was used for the construction of polyA sequencing libraries.
Illumina mRNA Sequencing Sample Preparation Guide, September 2009 (Amin et al, in review)

treatment_protocol: RNA from hearts was extracted using Trizol

tag: injected with

value: stage 44-45

value: 70-100 pooled hearts


title: Liver + LV, rep2

city: New York

first: Brian

last: Brown

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequence reads were filtered for low quality and mapped to the mm9 genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following the protocol from Mortazavi et al., Nat Methods, 2008 (PMID 18516045). Briefly, all reads falling in the exons of a given gene were counted and normalized by the length of the gene and the total reads of the run.
Genome_build: mm9
Supplementary_files_format_and_content: GSE39129_Liver+LV_consolidated.txt, which is linked to the Series record as a supplementary file, contains the number of reads per gene (RPKMs).

organism: Mus musculus

source_name: Liver, LV

extract_protocol: Total RNA was extracted from livers following the QIAzol protocol. The Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Mice were intravenously injected with 3x10^8 transducing units (TU) of a LV vector and sacrificed 4h later.

tag: tissue

value: liver

tag: treatment

value: lentiviral vector (LV)


title: Liver untreated, rep1

source_name: Liver, untreated


title: Liver + LV, rep3


title: wildtype, 1st replicate


title: Liver untreated, rep2


title: Control-45

description: Sample 1

value: Control-MO

value: control


title: Liver untreated, rep3


title: Liver + LV, rep1


title: mouse/plasmacytoma TEPC1165/4C;bait:IgH;enzyme:Hind/rep1

status: Public on Jul 04 2013

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: library strategy: 4C

data_processing: see "DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes" [PMID:22314321]

source_name: mouse plasmacytoma TEPC1165

tag: 4c protocol

tag: cell type

value: plasmacytoma TEPC1165

value: Balb/c


title: mouse/plasmacytoma PCT4961/4C;bait:IgH;enzyme:Hind/rep1

description: library strategy: 4C

source_name: mouse plasmacytoma PCT4961

extract_protocol: see "DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes" [PMID:22314321]

value: plasmacytoma PCT4961

tag: strain

value: AID-/- BclXL


title: mouse/plasmacytoma PCT6937/H3K9Ac/rep1

data_processing: Image analysis, base calling, quality filtering: Standard settings of GAPipeline using PhiX control; ***Raw data***: Fastq files contain full length reads that passed the chastity filter. Qualities were scaled to phred33 format for all files. ***Wig file***: Reads were aligned to the mouse genome (build mm9) with bowtie accepting only reads that had a unique match in the genome in their top quality stratum (bowtie 0.12.8, --best --all --strata -m1 -n2 -l50). Redundancy was capped at a maximum of 3 identically aligned reads, and reads shifted by half the approximate fragment size of 120 towards the fragment center were counted in 100 nt bins along the genome. Counts were normalized to the non redundant library size and bin size such that the final units are reads per kb per million (RPKM).

source_name: mouse plasmacytoma PCT6937

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H3K9Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol

tag: antibody

value: plasmacytoma PCT6937

value: mixed


title: mouse/plasmacytoma PCT4961/H4K91Ac/rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H4K91Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol

tag: genotype


title: mouse/plasmacytoma PCT4961/H4K8Ac/rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H4K8Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: mouse/plasmacytoma PCT4961/H3K36me2/rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H3K36me2 antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: mouse/plasmacytoma PCT4961/H2AZ/rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H2AZ antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: mouse/plasmacytoma PCT4961/RNASeq/rep1

data_processing: base calling and fastq file generation: Standard illumina pipeline tools; alignment: gsnap [--novelsplicing=0 --use-splicing=mm9.splices.iit --format=sam --batch=4] filtered to an alignment quality of 20 or more; wig file: Redundancy was capped at a maximum of 3 identically aligned reads and reads were counted in 100 nt bins along the genome. Counts were normalized to the non redundant library size and bin size such that the final units are reads per kb per million (RPKM).

extract_protocol: RNA was isolated with Trizol and libraries were generated with TrueSeq kits according to manufacturer's instructions.

value: RNASeq


title: mouse/plasmacytoma PCT4961/PolII/rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-PolII antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol

value: PolII


title: mouse/plasmacytoma PCT4961/H3K27Ac/rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H3K27Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: mouse/plasmacytoma PCT4961/H2BK5Ac/rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H2BK5Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: mouse/plasmacytoma PCT4961/H3K4me3/rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H3K4me3 antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: Normal Brain 3

description: small RNA

extract_protocol:
RNA was harvested from frozen brain tissue using Trizol reagent.
Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA.

value: brain (dorsolateral prefrontal cortex)

tag: gender

value: female

tag: disease state

value: normal


title: mouse/in vitro activated B cell/H2AZ/rep1

source_name: mouse, in vitro activated B cells

growth_protocol: CD43− B cells were isolated from spleens by immunomagnetic depletion (Miltenyi Biotech). Purified cells were then activated in RPMI-1640 media with 10% (vol/vol) FCS, 1×antibiotic-antimycotic, 1% (wt/vol) glutamine, 1× non-essential amino acids, 1% (wt/vol) sodium pyruvate, 53uM 2-beta-mercapto-ethanol, and 10 mM Hepes for 72 h in the presence of 50ug/mL of LPS (Escherichia coli 0111:B4; Sigma) and 2.5 ng/mL of IL-4 (Sigma).

value: in vitro activated B cells


title: ppc_mixed_GAII_smallRNA-seq

city: Berlin

first: Rina

last: Ahmed

address: Robert-Roessle-Strasse 10

country: Germany

institute: Max-Delbrueck-Center

data_processing:
Bad quality reads were filtered out (if quality score of each read was smaller than 10 in more than 10 positions) followed by read error correction using SAET 2.2 (SOLiD reads only).
Barcode sequences were detected (HiSeq lane) and adapter sequences removed by local Smith-Waterman alignment using FAR 1.8 (now FLEXBAR; Dodt et al. 2012, submitted).
Preprocessed short reads were aligned to the respective genomes using SHRiMP 2.1.1 (David et al. 2011) with local alignment mode and parameters -h 80% --strata –o 20 –max-alignments 20. Small RNA reads from C. elegans were allowed to map at most 10 times.
Genome_build: C. eleags: WormBase realse WS204. P. pacificus: in-house genome. S. ratti: genome version 1.
Supplementary_files_format_and_content: Tab-delimited text files include normalized miRNA expression values. Read counts were normalized by quantile based reference normalization (Schulte et al. 2010).

organism: Pristionchus pacificus

extract_protocol:
Total RNA was purified by Trizol Reagent (Invitrogen).
Small RNA library was generated according to the illumina v1.5 protocol for small RNA sequencing and subsequently sequenced using Illumina Genome Analyzer II.

value: RS2333 (formerly known as PS312)

tag: developmental stage

value: nematode whole worm


title: mouse/plasmacytoma PCT4961/H3K9Ac/rep1


title: mouse/plasmacytoma PCT4961/H2BK120Ac/rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H2BK120Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: cel_mixed_SOLiD_smallRNA-seq

extract_protocol:
Total RNA was purified by Trizol Reagent (Invitrogen).
Small RNA was enriched using FlashPAGE (Ambiont). The SOLiD Small RNA Expression Kit (Applied Biosystems) was used for preparation of cDNA and subsequently sequenced using the SOLiD technology.

value: N2 (Bristol)


title: mouse/in vitro activated B cell/H4K8Ac/rep1


title: mouse/in vitro activated B cell/H2BK5Ac/rep1


title: mouse/plasmacytoma PCT4961/4C;bait:IgH;enzyme:Hind/rep2

description: library strategy: 4C


title: mouse/in vitro activated B cell/H3K36me2/rep1


title: mouse/plasmacytoma TEPC1165/4C;bait:IgH;enzyme:Hind/rep2

description: library strategy: 4C


title: WCE_Day5_Seq

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: WCE control

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (version mm8) using Bowtie (Langmead et al Genome Biology 2009) version 0.9.9.2 with options -k 2 --best. Only uniquely mapping reads were analyzed further. Multiple hits aligning to the same nucleotide position are discarded above the level expected at a 10^-7 probability from a per-base Poisson model of the uniquely mappable portion of the mouse genome. In practice, this caps the number of hits that start at the same nucleotide to 3 in the RAR ChIP-seq experiments.
Peaks: Binding event detection is carried out using a customized methodology named SEEDS (Sequencing Experiment Event Detection Statistics) that uses statistical significance testing to find regions producing an over-abundance of sequenced reads in the signal experiments compared with the control. The algorithm is run twice across the data. The first pass estimates a scaling factor for control sequencing read depth and a model of the distribution of sequencing read alignment hits around binding events. The second pass applies these parameters to predict a final set of significant events. Before the first pass, the scaling factor is initialized to be the ratio of total hit counts between the signal and control channels. The binding distribution model is initialized to be an empirical distribution estimated around predicted binding events in Oct4 ChIP-seq data (Marson, et al. Cell 2008). All alignment hits are extended in both 3’ and 5’ directions, mirroring the observed distribution of hits around binding events. The extension magnitudes are set equal to the positions where the binding model distribution intersects a uniform distribution over the same area. Control channel hit counts are scaled using the signal-control scaling factor. A sliding window of bin width 50bp and offset 25bp is run over the genome. Overlapping extended hit counts are calculated for both the signal and (scaled) control channels. The background distribution of ChIP-seq hits is modeled as a non-homogenous Poisson process with parameters estimated from the scaled control hit counts. Specifically, the Poisson parameter is chosen as the maximum mean overlapping hit count in 50bp windows of those observed from i) the entire genome, ii) a 5Kbp window centered on the current location, and iii) a 10Kbp window centered on the current location. The use of this dynamic background model is motivated by the desire to correct local ChIP-seq enrichment biases that appear in the signal and control channels, and is similar to the model employed by MACS (Zhang, et al. Genome Biol 2008). A given bin is denoted as potentially enriched if the overlapping hit count exceeds that expected from the background model at a p-value of 10^-9. P-values for each potentially enriched bin’s over-representation in the signal channel over the control are calculated using the binomial distribution CDF (see Rozowsky, et al. Nature Biotech 2009). Neighboring regions in the set of potentially enriched regions are merged, and the maximal p-value observed for the constituent bins is attached to the resulting merged region. The p-values are corrected for multiple hypothesis testing using Benjamini & Hochberg’s method, and all regions with corrected p-values above 0.001 are discarded. False-discovery rates are estimated by repeating the event discovery procedures after swapping the scaled control channel and the signal channel. After the first pass, the scaling factor is estimated by carrying out linear regression on the hit counts observed in 10,000 bp windows that are devoid of potentially significant events in both the signal and control channels. The binding model is estimated from enriched regions with p-values < 10^-7 and signal/control hit count enrichment greater than 10. These regions are aligned around the 'peak' location, defined as the position of maximum probability when scanning the current binding model over the region's hit landscape.

source_name: Day5 motor neurons

growth_protocol: ES cells were differentiated as previously described (Wichterle, et al. Cell 2002).  Briefly, ES cells were trypsinized and seeded at 5x10e5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 1, Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x10e7 cells on Day 0. An inducible Cdx2-V5 line was made by inserting the appropriate coding sequence followed by a his-V5 tag peptide in the LoxP of the Ainv15 cell line (ATCC SCRC-1029). Induction of the transgenes was done by adding 2ug/ml of Doxycycline for ~30 hours

extract_protocol: ChIP protocols were adapted from http://jura.wi.mit.edu/young_public/hESregulation/ChIP.html.  Descriptions of these protocol modifications have been previously published (Guenther, et al., Genes Dev 2008). Briefly, approximately 6x10e7 cells taken from each developmental time point were cross-linked using formaldehyde and snap-frozen in liquid nitrogen.  Cells were thawed on ice, resuspended in 5ml lysis buffer 1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and mixed on a rotating platform at 4°C for 5 minutes.  Samples were spun down for 3 minutes at 3000rpm, resuspended in 5ml lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and mixed on a rotating platform for 5 minutes at room temperature.  Samples were spun down once more, resuspended in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp.  Triton X-100 was added to the lysate after sonication to final concentrations of 1% and the lysate spun down to pellet cell debris.  The resulting whole-cell extract supernatant was incubated on a rotating mixer overnight at 4°C with 100 µL of Dynal Protein G magnetic beads that had been preincubated for 24 hours with 10 µg of the appropriate antibody in a PBS/BSA solution. Pol2-S5P (Abcam, ab5131), Olig2 (Millipore, ab9610), and anti-V5 (Abcam, ab15828) antibodies were used for ChIP experiments. After approximately 16 hours of bead-lysate incubation, beads were collected with a Dynal magnet.  ChIP samples probing for transcription factor binding were washed with the following regimen, mixing on a rotating mixer at 4°C for 5 minutes per buffer: low-salt buffer (20 mM Tris at pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high-salt buffer (20 mM Tris at pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10 mM Tris at pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% deoxycholate, 1% NP-40), and TE containing 50 mM NaCl.  ChIP samples probing for histone and chromatin marks were washed 4 times with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and then once with TE containing 50 mM NaCl, again mixing on a rotating mixer at 4°C for 5 minutes per buffer.  After the final bead wash, samples were spun down to collect and discard excess wash solution, and bound antibody-protein-DNA fragment complexes were eluted from the beads by incubation in elution buffer at 65°C with occasional vortexing.  Cross-links were reversed by overnight incubation at 65°C.  Samples were digested with RNase A and Proteinase K to remove proteins and contaminating nucleic acids, and the DNA fragments precipitated with cold EtOH. Purified DNA fragments were processed according to a modified version of the Illumina/Solexa sequencing protocol (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Ectopic exposure to retinoic acid and hedgehog agonist at day 2 during the differentiation protocol. FGF signalling treatment for Cdx2 experiments

value: Ainv15 (ATCC SCRC-1029)

tag: cell stage

tag: chip-antibody

value: WCE


title: ChIP-seq analysis of Isl1/2 in iI induced cells (Day 4)

description: Chromatin IP against Isl1/2

data_processing:
Basecalling: Performed with CASAVA v1.7
Alignment: Sequence reads were aligned to the mouse genome (version mm9) using Bowtie (Langmead, et al. Genome Biology 2009) version 0.12.5 with options "-q --best --strata -m 1 -p 4 --chunkmbs 1024". Only uniquely mapping reads were analyzed further. All alignment data is provided here in BAM format.
Peaks: Binding events were detected using GPS (Guo, et al. Bioinformatics 2010) version 2.0. In GPS, the scaling ratio between IP and control channels was estimated using the median ratio of all 10Kbp windows along the genome. The GPS binding model was initialized to the default and iteratively updated over up to 3 training rounds. In this study, we require that reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the control level with p-value <0.01 as tested using the Binomial distribution. Signal-to-noise ratios are estimated by comparing the ChIP-seq read count occurring at any peak found for a given transcription factor in any condition to the count of remaining reads in that experiment. Peaks are provided here in two formats, BED and GPS raw output. The BED format shows the GPS-predicted binding position, and the Q-value calculated by GPS is provided in the score field. The GPS raw output has the following fields (tab-separated): 1) Binding event coordinate, 2) IP read count assigned to event, 3) Control read count assigned to event, 4)Fold enrichment (IP/Control), 5) Q-value (multiple hypothesis corrected), 6) P-value, 7) Shape deviation from the empirical read distribution (log10(KL)), 8) Shape deviation between IP vs Control (log10(KL)).
BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts. Read counts per starting base pair were limited to 1 in the Isl1-2_iMN_Day4 and Isl1-2_iIsl-Day4 experiments due to lower library complexity than sequencing depth. WIG files were converted to bigWig using wigToBigWig (UCSC).
Genome_build: mm9
Supplementary_files_format_and_content: alignment files are BAM format output from Bowtie; bigwig files are generated from aligned reads as described in the data processing steps; peaks are provided in two formats: a) standard BED format where the size of each peak is 1bp centered on the GPS prediction and where the score field represents the GPS Q-value, and b) "*.gps.txt" files which are tab-delimited output from GPS.

source_name: Isl1 induced cells (Day4 iI differentiation)

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM ?-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described.  Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x105 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x107 cells on Day 0. Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

extract_protocol: Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. Pellets containing ~40 x106 cells were flash frozen and stored at -80 oC. Cells were thawed on ice, resuspended in 5ml of Lysis Buffer A and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 5ml Lysis Buffer B and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 3ml of Sonication Buffer (SB). Nuclear extracts were sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp. Sonicated chromatin was incubated for 16 hours at 4C with Protein-G beads (Invitrogen) conjugated with either rabbit anti-V5 (Abcam) or anti-Isl1 monoclonal antibodies are a generous gift from Dr. T. Jessell (Columbia University). After incubation and with the aid of a magnetic device, beads were washed once with SB+500nM NaCl, once with LiCl Wash Buffer and 1ml of TE. Then, beads were centrifugated at 950g for 3 min and remove residual TE with a pipette. 210ul of Elution Buffer was added to the beads followed by incubation at 65 oC for 45 minutes with a brief pulse of vortex every 10 minutes. 200ul of supernatant was removed after a 1 minute centrifugation at 16,000g. The crosslink was reversed by 16 hours incubation at 65 oC.  RNA was digested by the addition of 200ul of TE and RNAseA (Sigma) at a final concentration of 0.2mg/ml and incubated for 2 hours at 37C.  Protein was digested by the addition of Proteinase K (0.2 mg/ml final, Invitrogen) supplemented with CaCl2 followed by a 30 minutes incubation at 55 oC. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70ul of water. Purified DNA fragments were processed according to the Illumina/Solexa library  protocol and sequenced using a Genome Analyzer II (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

tag: cell line

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible Isl1-V5 construct

tag: cell treatment

value: +Dox 48hrs

tag: chip antibody

value: anti-Isl1/2 (gift from Dr. T. Jessell)


title: ChIP-seq analysis of induced V5-tagged Phox2a (iPhox2a-V5) in iNIP induced cortical motor neurons (Day 4)

description: Chromatin IP against V5

source_name: induced cortical motor neurons (Day4 iNIP differentiation)

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible Ngn2.Isl1.Phox2a-V5 construct

value: anti-V5 (Abcam, ab15828)


title: ChIP-seq analysis of Isl1/2 in iNIP induced cortical motor neurons (Day 4)

description: Chromatin IP against Isl1/2

value: induced cortical motor neurons (Day4 iNIP differentiation)


title: Pseudo-ChIP control using anti-V5 in progenitor motor neurons (Day_4)

description: progenitor motor neurons (Day4 directed differentiation)

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (version mm9) using Bowtie (Langmead, et al. Genome Biology 2009) version 0.12.5 with options "-q --best --strata -m 1 -p 4 --chunkmbs 1024". Only uniquely mapping reads were analyzed further. All alignment data is provided here in BAM format.
Peaks: Binding events were detected using GPS (Guo, et al. Bioinformatics 2010) version 1.0. In GPS, the scaling ratio between IP and control channels was estimated using the median ratio of all 10Kbp windows along the genome. The GPS binding model was initialized to the default and iteratively updated over up to 3 training rounds. In this study, we require that reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the control level with p-value <0.01 as tested using the Binomial distribution. Signal-to-noise ratios are estimated by comparing the ChIP-seq read count occurring at any peak found for a given transcription factor in any condition to the count of remaining reads in that experiment. Peaks are provided here in two formats, BED and GPS raw output. The BED format shows the GPS-predicted binding position, and the Q-value calculated by GPS is provided in the score field. The GPS raw output has the following fields (tab-separated): 1) Binding event coordinate, 2) IP read count assigned to event, 3) Control read count assigned to event, 4)Fold enrichment (IP/Control), 5) Q-value (multiple hypothesis corrected), 6) P-value, 7) Shape deviation from the empirical read distribution (log10(KL)), 8) Shape deviation between IP vs Control (log10(KL)).
WIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts.

source_name: Pseudo IP against V5

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described (Wichterle, et al. Cell 2002).  Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x105 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 1, Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 ÂµM all-trans-Retinoic acid (RA, Sigma) and 0.5 ÂµM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0. Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

extract_protocol: Differentiating embryoid bodies were washed with PBS and then dissociated by mild Trypsinization (Invitrogen) followed by mechanical dissociation until single-cell suspension was obtained. Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. Pellets containing ~40 x106 cells were flash frozen and stored at -80 oC. Cells were thawed on ice, resuspended in 5ml of Lysis Buffer A and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 5ml Lysis Buffer B and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 3ml of Sonication Buffer (SB). Nuclear extracts were sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp. Sonicated chromatin was incubated for 16 hours at 4C with Protein-G beads (Invitrogen) conjugated with either rabbit anti-V5 (Abcam), mouse anti-Flag M2 (Sigma) or rabbit anti-Olig2 (Millipore). After incubation and with the aid of a magnetic device, beads were washed once with SB+500nM NaCl, once with LiCl Wash Buffer (LiClB) and 1ml of TE. Then, beads were centrifugated at 950g for 3 min and remove residual TE with a pipette. 210ul of Elution Buffer was added to the beads followed by incubation at 65 oC for 45 minutes with a brief pulse of vortex every 10 minutes. 200ul of supernatant was removed after a 1 minute centrifugation at 16,000g. The crosslink was reversed by 16 hours incubation at 65 oC.  RNA was digested by the addition of 200ul of TE and RNAseA (Sigma) at a final concentration of 0.2mg/ml and incubated for 2 hours at 37C.  Protein was digested by the addition of Proteinase K (0.2 mg/ml final, Invitrogen) supplemented with CaCl2 followed by a 30 minutes incubation at 55 oC. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70ul of water. Purified DNA fragments were processed according to the Illumina/Solexa sequencing protocol using a Genome Analyzer II (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 ÂµM all-trans-Retinoic acid (RA, Sigma) and 0.5 ÂµM agonist of hedgehog signaling (SAG, Calbiochem). Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

value: Ainv15 (ATCC SCRC-1029) with inducible V5-tagged Olig2


title: WCE_Day5-Seq

description: WCE control


title: H3K79me2 in progenitor motor neurons [ChIP-seq]

description: Chromatin IP against H3K79me2

data_processing:
Basecalling: Performed with CASAVA v1.7
BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts. WIG files were converted to bigWig using wigToBigWig (UCSC).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files are generated from aligned reads as described in the data processing steps.

source_name: progenitor motor neurons

growth_protocol: ES cells were differentiated as previously described (Wichterle, et al. Cell 2002).  Briefly, ES cells were trypsinized and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 1 and Day 2 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.

extract_protocol: ChIP protocols were adapted from http://jura.wi.mit.edu/young_public/hESregulation/ChIP.html.  Descriptions of these protocol modifications have been previously published (Guenther, et al., Genes Dev 2008). Briefly, approximately 6x10^7 cells taken from each developmental time point were cross-linked using formaldehyde and snap-frozen in liquid nitrogen.  Cells were thawed on ice, resuspended in 5ml lysis buffer 1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and mixed on a rotating platform at 4°C for 5 minutes.  Samples were spun down for 3 minutes at 3000rpm, resuspended in 5ml lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and mixed on a rotating platform for 5 minutes at room temperature.  Samples were spun down once more, resuspended in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp.  Triton X-100 was added to the lysate after sonication to final concentrations of 1% and the lysate spun down to pellet cell debris.  The resulting whole-cell extract supernatant was incubated on a rotating mixer overnight at 4°C with 100 µL of Dynal Protein G magnetic beads that had been preincubated for 24 hours with 10 µg of the appropriate antibody in a PBS/BSA solution. After approximately 16 hours of bead-lysate incubation, beads were collected with a Dynal magnet.  ChIP samples probing for transcription factor binding were washed with the following regimen, mixing on a rotating mixer at 4°C for 5 minutes per buffer: low-salt buffer (20 mM Tris at pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high-salt buffer (20 mM Tris at pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10 mM Tris at pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% deoxycholate, 1% NP-40), and TE containing 50 mM NaCl.  ChIP samples probing for histone and chromatin marks were washed 4 times with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and then once with TE containing 50 mM NaCl, again mixing on a rotating mixer at 4°C for 5 minutes per buffer.  After the final bead wash, samples were spun down to collect and discard excess wash solution, and bound antibody-protein-DNA fragment complexes were eluted from the beads by incubation in elution buffer at 65°C with occasional vortexing.  Cross-links were reversed by overnight incubation at 65°C.  Samples were digested with RNase A and Proteinase K to remove proteins and contaminating nucleic acids, and the DNA fragments precipitated with cold EtOH. Purified DNA fragments were processed according to a modified version of the Illumina/Solexa sequencing protocol (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Ectopic exposure to retinoic acid and hedgehog agonist at day 2 during the differentiation protocol.

tag: cell-treatment

value: +RA +Hh

tag: cell-stage

value: progenitor motor neurons (Day 4)

value: anti-H3K79me2 antibody (Abcam ab3594)


title: H3K27me3 in progenitor motor neurons [ChIP-seq]

description: Chromatin IP against H3K27me3

value: anti-H3K27me3 (Abcam, ab6002)


title: H3K4me3 in progenitor motor neurons [ChIP-seq]

description: Chromatin IP against H3K4me3

value: anti-H3K4me3 antibody (Abcam ab8580)


title: H3K27me3 in RA/Hh-derived motor neurons (Day5) exposed to RA and Hh [ChIP-Seq]

description: Chromatin IP against H3K27me3

data_processing:
Basecalling: Performed with CASAVA v1.7
BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts. Read counts per starting base pair were limited to 1 in the H3K27me3 experiments due to lower library complexity than sequencing depth. WIG files were converted to bigWig using wigToBigWig (UCSC).
Peaks: TF binding events were detected using GPS (Guo, et al. Bioinformatics 2010) version 2.0. In GPS, the scaling ratio between IP and control channels was estimated using the median ratio of all 10Kbp windows along the genome. The GPS binding model was initialized to the default and iteratively updated over up to 3 training rounds. In this study, we require that reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the control level with p-value <0.01 as tested using the Binomial distribution. Signal-to-noise ratios are estimated by comparing the ChIP-seq read count occurring at any peak found for a given transcription factor in any condition to the count of remaining reads in that experiment.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files are generated from aligned reads as described in the data processing steps.

source_name: motor neurons (Day 5)

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described.  Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0).  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox)  (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.

extract_protocol: Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. Pellets containing ~40 x10^6 cells were flash frozen and stored at -80 oC. Cells were thawed on ice, resuspended in 5ml of Lysis Buffer A and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 5ml Lysis Buffer B and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 3ml of Sonication Buffer (SB). Nuclear extracts were sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp. Sonicated chromatin was incubated for 16 hours at 4C with Protein-G beads (Invitrogen) conjugated with either rabbit anti-V5 (Abcam) or anti-H3K27me3 (Abcam). After incubation and with the aid of a magnetic device, beads were washed once with SB+500nM NaCl, once with LiCl Wash Buffer and 1ml of TE. Then, beads were centrifugated at 950g for 3 min and remove residual TE with a pipette. 210ul of Elution Buffer was added to the beads followed by incubation at 65 oC for 45 minutes with a brief pulse of vortex every 10 minutes. 200ul of supernatant was removed after a 1 minute centrifugation at 16,000g. The crosslink was reversed by 16 hours incubation at 65 oC.  RNA was digested by the addition of 200ul of TE and RNAseA (Sigma) at a final concentration of 0.2mg/ml and incubated for 2 hours at 37C.  Protein was digested by the addition of Proteinase K (0.2 mg/ml final, Invitrogen) supplemented with CaCl2 followed by a 30 minutes incubation at 55 oC. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70ul of water. Purified DNA fragments were processed according to the Illumina/Solexa library  protocol and sequenced using a Genome Analyzer II (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3  when required.

tag: cell-line

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct

value: motor neurons (Day 5)


title: H3K27me3 in RA/Hh-derived motor neurons (Day5) exposed to Dox(iCdx2), RA, Hh and FGF [ChIP-Seq]

description: Chromatin IP against H3K27me3

value: +RA +Hh +Dox +FGF


title: induced V5-tagged Cdx2 (iCdx2-V5) in RA/Hh-derived progenitor motor neurons (Day4) exposed to Dox but not FGF [ChIP-Seq]

description: Chromatin IP against V5

source_name: progenitor motor neurons (Day 4)

value: +RA +Hh +Dox


title: H3K27me3 in Day5 cells exposed to Dox(iCdx2) and FGF [ChIP-Seq]

description: Chromatin IP against H3K27me3

source_name: Day 5 cells

value: +Dox +FGF

value: Day 5


title: mouse/plasmacytoma PCT4961/H2BK5Ac/rep2

value: plasmacytoma PCT4961

value: Balb/c

value: AID-/- BclXL


title: mouse/plasmacytoma PCT4961/H3K36me2/rep2


title: cel_mixed_GAII_smallRNA-seq

value: N2 (Bristol)

value: mixed

tag: tissue

value: nematode whole worm


title: mouse/plasmacytoma PCT4961/H3K4me3/rep2


title: mouse/plasmacytoma PCT4961/H3K27Ac/rep2


title: induced V5-tagged Cdx2 (iCdx2-V5) in RA/Hh-derived progenitor motor neurons (Day4) exposed to Dox and FGF [ChIP-Seq]

description: Chromatin IP against V5

value: anti-V5 (Abcam, ab15828)


title: mouse/plasmacytoma PCT4961/H3K9Ac/rep2

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H3K9Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: Pol2 in progenitor motor neurons [ChIP-seq]

description: Chromatin IP against Pol2

value: +RA +Hh

value: progenitor motor neurons (Day 4)

value: anti-Pol2 antibody 8WG16 (Covance MMS-126R)


title: mouse/plasmacytoma PCT4961/H4K91Ac/rep2

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H4K91Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: ChIP-seq analysis of Isl1/2 in iNIL3 induced motor neurons (Day 4)

description: Chromatin IP against Isl1/2

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (version mm9) using Bowtie (Langmead, et al. Genome Biology 2009) version 0.12.5 with options "-q --best --strata -m 1 -p 4 --chunkmbs 1024". Only uniquely mapping reads were analyzed further. All alignment data is provided here in BAM format.
Peaks: Binding events were detected using GPS (Guo, et al. Bioinformatics 2010) version 1.0. In GPS, the scaling ratio between IP and control channels was estimated using the median ratio of all 10Kbp windows along the genome. The GPS binding model was initialized to the default and iteratively updated over up to 3 training rounds. In this study, we require that reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the control level with p-value <0.01 as tested using the Binomial distribution. Signal-to-noise ratios are estimated by comparing the ChIP-seq read count occurring at any peak found for a given transcription factor in any condition to the count of remaining reads in that experiment. Peaks are provided here in two formats, BED and GPS raw output. The BED format shows the GPS-predicted binding position, and the Q-value calculated by GPS is provided in the score field. The GPS raw output has the following fields (tab-separated): 1) Binding event coordinate, 2) IP read count assigned to event, 3) Control read count assigned to event, 4)Fold enrichment (IP/Control), 5) Q-value (multiple hypothesis corrected), 6) P-value, 7) Shape deviation from the empirical read distribution (log10(KL)), 8) Shape deviation between IP vs Control (log10(KL)).
BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts. Read counts per starting base pair were limited to 1 in the Isl1-2_iMN_Day4 eexperiment due to lower libnrary complexity than sequencing dpeth. WIG files were converted to bigWig using wigToBigWig (UCSC)

source_name: induced motor neurons (Day4 iNIL differentiation)

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described.  Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x105 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 uM all-trans-Retinoic acid (RA, Sigma) and 0.5 uM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x107 cells on Day 0. Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

treatment_protocol: Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 uM all-trans-Retinoic acid (RA, Sigma) and 0.5 uM agonist of hedgehog signaling (SAG, Calbiochem). Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible Ngn2.Isl1.Lhx3-V5 construct

value: +Dox 48hrs

value: anti-Isl1/2 (gift from Dr. T. Jessell)


title: ChIP-seq analysis of induced V5-tagged Lhx3 (iLhx3-V5) in iNIL3 induced motor neurons (Day 4)

description: Chromatin IP against V5

value: induced motor neurons (Day4 iNIL differentiation)


title: mouse/plasmacytoma PCT4961/H2BK120Ac/rep2


title: mouse/plasmacytoma PCT4961/H2AZ/rep2

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H2AZ antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: mouse/in vitro activated B cell/H4K91Ac/rep1

value: in vitro activated B cells


title: mouse/plasmacytoma PCT4961/H4K8Ac/rep2

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H4K8Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: mouse/in vitro activated B cell/H2AZ/rep2


title: mouse/in vitro activated B cell/H2BK120Ac/rep1


title: mouse/in vitro activated B cell/H3K36me2/rep2

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H3K36me2 antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol


title: cel_dauer_HiSeq_smallRNA-seq

extract_protocol:
Total RNA was purified by Trizol Reagent (Invitrogen).
Small RNA library was generated by NEXTflex small RNA sequencing kit (Bioo Scientific) and subsequently sequenced using Illumina HiSeq 2000.

value: dauer


title: Reg- amputated C3

city: San Francisco

first: James

last: Sikes

address: 2130 Fulton Street

department: Biology

institute: University of San Francisco

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads Per Kiloase of transcript per Million mapped reads were determined using the RNAseq module in CLC Genomics Workbench (version 4) using default settings.
Samples were mapped to a de novo transcriptome (GAKZ00000000).
Genome_build: TSA GAKZ00000000
Supplementary_files_format_and_content: Table includes RPKM values and other important metrics (e.g., total gene reads) for each sample.

organism: Procotyla fluviatilis

source_name: excised body tissues at posterior amputation site, Reg-

growth_protocol: Worms were field collected and cultured for short periods in the laboratory at 18C before amputation and RNA extraction.

extract_protocol:
Total RNA was prepared from pools of 3 worms using Trizol (Invitrogen, Carlsbad, CA) and DNase treatment (DNA-free RNA kit, Zymo Research, Irvine, CA).
Libraries were constructed using the TruSeq RNAseq Sample Prep kit. The libraries were quantitated by qPCR, pooled and sequenced on four lanes for 100 cycles on an Illumina HiSeq 2000 using a TruSeq SBS sequencing kit version 3.

treatment_protocol: Worms were amputated at body regions either anterior or posterior to the pharynx. Tissues were excised posterior to the amputation site 24 hours after lesion.

tag: regeneration proficiency

value: deficient

value: adult

tag: treatment

value: amputated posterior to pharynx

value: near amputation site


title: Reg- amputated C2


title: Reg+ uncut B3

source_name: excised body tissues at comparable anterior amputation site, Reg+

value: proficient

value: uncut

value: comparable anterior amputation site


title: Reg- uncut D3

source_name: excised body tissues at comparable posterior amputation site, Reg-

value: comparable posterior amputation site


title: Reg- amputated C1


title: Reg- uncut D1


title: Reg- uncut D4


title: Reg+ uncut B1


title: Reg+ uncut B2


title: Reg+ amputated A2

source_name: excised body tissues at anterior amputation site, Reg+

value: amputated anterior to pharynx


title: Reg+ amputated A3


title: ppc_dauer_HiSeq_smallRNA-seq

tag: strain

value: RS2333 (formerly known as PS312)

value: nematode whole worm


title: str_iL3_GAII_smallRNA-seq

organism: Strongyloides ratti

value: Basel (Dr. G. Pluschke; Swiss Tropical Insitute)

value: infective larvae


title: ppc_mixed_HiSeq_smallRNA-seq

value: mixed


title: str_mixed_GAII_smallRNA-seq


title: mouse/in vitro activated B cell/H4K8Ac/rep2

tag: antibody

tag: cell type


title: Reg+ amputated A1


title: ppc_mixed_SOLiD_smallRNA-seq


title: cel_mixed_HiSeq_smallRNA-seq

value: N2 (Bristol)


title: RLPII_phospho2_ab5095.Clone_8.Solexa ChIP Rep2

status: Public on Jul 03 2013

data_processing: Bowtie alignment protocol. Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.Reads that passed default parameters of the Illumina quality filter were mapped with Bowtie 0.12.7. The reference sequence used to built an index for mapping was the Flybase reference r5.22. The reference index was created using the bowtie-build function with default parameters. Reads were mapped using  -n 2 -l 28 -e 70 -k 1 -m 10 --best in Bowtie (-n 2, -l 28, -e 70 default). Parameters-n INT number of allowed mismatch-l INT seed length-e INT maximum permitted total of quality values at all mismatched read positions-m INT suppress all alignments for a particular read or pair if more than INT reportable alignments-k INT report up to INT valid alignments--best report alignments in best-to worst orderReads were converted to SAM formant using the bowtie2sam.pl script provided by the DCC. SPP Peak calling protocol. The aligned reads were called using SPP R package (ver.1.10, Kharchenko et al., Nat.Biotech 2008). The binding characteristics and tag shift were estimated using SPP get.binding.characteristics() function. The reads showing abnormality were removed using SPP remove.local.tag.anomalies() function. The regions of enrichment were identified as continuous blocks of positions that exhibit significant enrichment of IP over input reads. The significance of enrichment was assessed within a 1Kb window around each point using a Poisson model. A position was considered significantly enriched if the number of IP read counts was significantly higher (Z-score > 3) than the number of input read counts, after adjusting for the total number of reads sequenced in IP and input measurements. For each replicate set, if replicates were consistent (>80% agreement for top 40% of peaks/enrichment clusters), reads in each replicates were combined and enrichment regions were called as described above.  Processed data are obtained using following parameters: genome version is FlyBase r5

organism: Drosophila melanogaster

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: dorsal mesothoracic disc

value: third instar larval stage

tag: Sex

value: Male


title: Restorer line 121C

city: Beijing

first: Chen

last: Liu

address: Yuanmingyuan West Road 2#, Haidian District

institute: China Agricultural University

data_processing:
Raw data was scanned using Casava with default parameters, and reads with more 10% Q<20 bases were removed.
All sequences smaller than 70 bases were eliminated.
High quality reads were assembled by Trinity with default parameters.
Reads number of each unigene was firstly transformed into RPKM and then differently expressed unigenes were identified by DEGseq package using the method MARS (MA-plot-based method with Random Sampling model). “FDR ≤ 0.001 and the absolute value of log2Ratio ≥ 1” was used as the threshold to judge the significance of unigene expression difference.
Supplementary_files_format_and_content: A tab-delimited excel file include RPKM values for each Sample. The fasta file includes the assembled transcriptome.

organism: Capsicum annuum

source_name: Anther

extract_protocol:
Anthers were taken out and frozen in liquid nitrogen and total RNA was isolated using Trizol reagent.RNA was incubated with DNase I, and messenger RNA was further purified with MicroPoly(A) Purist Kit as per the protocol and the final concentration was determined using NonoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Anther

tag: phenotype

value: restorer line


title: RLPII_phospho2_ab5095.Clone_8.Solexa Input Rep1

tag: developmental stage


title: RLPII_phospho2_ab5095.Clone_8.Solexa Input Rep2


title: RLPII_phospho2_ab5095.Clone_8.Solexa ChIP Rep1


title: CMS line 121A

value: cytoplasmic male sterility line


title: RPLII_ab5408.Kc.Solexa ChIP Rep1

source_name: RPLII_ab5408.Kc ChIP expt.2457

value: embryo-derived cell-line

value: late embryonic stage

tag: genotype

value: se/e

value: Female


title: Two S. cerevisiae strains containing D. hansenii YAC direct RNA sequences

city: Boston

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

data_processing:
alignment to genome (Helicos Helisphere)
separation of unambiguous data by yeast species
counting of sequence tags by coordinate on each strand
classification of coordinates by associated ORF on appropriate strand
Saccharomyces cerevisiae genome build 61 (2008/06/05); D. hansenii genome release 2 (2008/09/10); K. lactis version CR382121.1 (2004/07/03)
Genome_build: Saccharomyces cerevisiae genome build 61 (2008/06/05); D. hansenii genome release 2 (2008/09/10); K. lactis version CR382121.1 (2004/07/03)
Genome_build: Genome build: Saccharomyces cerevisiae: SGD genome build 61 (2008/06/05), version S288C_reference_genome_R61-1-1_20080605.tgz; http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/.
Genome_build: Genome build: D. hansenii: ASM644v1
Supplementary_files_format_and_content: Tab-delimited text files of tag counts at each coordinate in the 400 nt downstream of each ORF.

source_name: Saccharomyces cerevisiae harboring Debaryomyces hansenii DNA on YACs

growth_protocol: Cells were cultured  to mid-log phase in rich medium (YPD for S. cerevisiae).

extract_protocol:
Total RNA was isolated by the hot acidic phenol method and purified with DNase treatment on Qiagen RNeasy columns.
RNA sequenced directly by Helicos (DRS method); purified RNA was not modified

tag: direct rna sequence from

tag: s. cerevisiae strain 1

tag: s. cerevisiae strain 2

tag: culture protocol

value: Two Saccharomyces cerevisiae strains harboring Debaryomyces hansenii YACs were cultured separately and pooled into one sequencing lane


title: RPLII_ab5408.Kc.Solexa Input Rep2

source_name: RPLII_ab5408.Kc Input expt.2432

tag: cell line


title: RPLII_ab5408.Kc.Solexa ChIP Rep2

source_name: RPLII_ab5408.Kc ChIP expt.2458


title: H3K9ac.L3.Solexa ChIP Rep2

source_name: H3K9ac.L3 ChIP expt.2411

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

value: 3rd Instar Larvae

value: wild type


title: HP1b_(Henikoff).L3.Solexa Input Rep2

source_name: HP1b_(Henikoff).L3 Input expt.2224


title: HP1b_(Henikoff).L3.Solexa ChIP Rep2

source_name: HP1b_(Henikoff).L3 ChIP expt.2252


title: HP1b_(Henikoff).L3.Solexa Input Rep1

source_name: HP1b_(Henikoff).L3 Input expt.2222


title: HP1b_(Henikoff).L3.Solexa ChIP Rep1

source_name: HP1b_(Henikoff).L3 ChIP expt.2251


title: H3K9ac.L3.Solexa Input Rep2

source_name: H3K9ac.L3 Input expt.2226


title: H3K9ac.L3.Solexa Input Rep1

source_name: H3K9ac.L3 Input expt.2225


title: H1.L3.Solexa Input Rep2

source_name: H1.L3 Input expt.2404


title: H1.L3.Solexa ChIP Rep1

source_name: H1.L3 ChIP expt.2398


title: dSFMBT_Q2642.L3.Solexa ChIP Rep1

source_name: dSFMBT_Q2642.L3 ChIP expt.2425


title: H1.L3.Solexa Input Rep1

source_name: H1.L3 Input expt.2402


title: H1.L3.Solexa ChIP Rep2

source_name: H1.L3 ChIP expt.2399


title: dSFMBT_Q2642.L3.Solexa ChIP Rep2

source_name: dSFMBT_Q2642.L3 ChIP expt.2426


title: dSFMBT_Q2642.L3.Solexa Input Rep1

source_name: dSFMBT_Q2642.L3 Input expt.2330


title: Hras-G12V replicate 1

city: Seattle

first: Slobodan

last: Beronja

address: PO Box 19024, Mailstop D4-100

institute: Fred Hutchinson Cancer Research Center

data_processing:
RNA-seq reads were aligned to the genome using Tophat with defult settings.  Trapnell et al.
Transcript assembly and differential expression were determined using Cufflinks using Refseq mRNAs to guide assembly.  Trapnell et al.
Anaylsis of RNA-seq data was done in R using CummeRbund analysis package.  Trapnell et al.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: epidermal progenitors

extract_protocol:
FACS isolated cells were sorted directly into TrizolLS and RNA was extracted using Direct-Zol RNA Miniprep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols at Weill Cornel Medical School Genomics Core Facility

value: embryonic day 18.5 (E18.5)


title: dSFMBT_Q2642.L3.Solexa Input Rep2

source_name: dSFMBT_Q2642.L3 Input expt.2331


title: Hras-G12V Mllt6KD replicate 2

value: HrasG12V depleted of Mllt6


title: RPLII_ab5408.Kc.Solexa Input Rep1

source_name: RPLII_ab5408.Kc Input expt.2431


title: Hras-G12V Mllt6KD replicate 1


title: Control replicate 1

value: wild-type


title: S. cerevisiae and D. hansenii direct RNA sequence

organism: Debaryomyces hansenii

source_name: Saccharomyces cerevisiae and Debaryomyces hansenii

tag: s. cerevisiae strain

tag: d. hansenii strain

value: Strains were cultured separately and pooled into one sequencing lane.  AB1380 is the non-YAC-containing S. cerevisiae parental strain for JYAC06 and JYAC07.


title: Hras-G12V replicate 2


title: Hras-G12V Ctnnb1KD replicate 1

value: HrasG12V depleted of Ctnnb1