title: RN4220_ORF67

first: Joseph

last: Osmundson

address: 1230 York Ave

department: Molecular Biophysics

institute: The Rockefeller University

data_processing:
Read alignment using TopHat using NCTC8325 as a reference.  Reads aligning to multiple locations are kept (to a maximum of 20 potential positions) to assist constructing gene models for genes with repetitive or low complexity features. When aligning reads, 2 mismatches to the reference (Ensembl S_aureus_nctc_8325.EB1.fa) were allowed
Alignments reported from TopHat were processed by the Cufflinks software package to determine differential expression of genes and transcripts between conditions.
Wig files made from Tophat accepted_hits bam files using IGVTools with 25bp windows
Genome_build: Staphylococcus aureus NCTC8325 (Ensembl S_aureus_nctc_8325.EB1.fa)
Supplementary_files_format_and_content: wig

organism: Staphylococcus aureus

source_name: Staphylococcus aureus RN4220

extract_protocol:
RNA purified by modified Qiagen RNeasy kit
Illumina

tag: growth phase

value: early-log growth

value: pRMC2 with ORF67


title: NCTC8325-4

status: Public on Nov 07 2013

type: SRA

city: New York

state: NY

country: USA

library_source: transcriptomic

molecule: total RNA

source_name: Staphylococcus aureus NCTC8325-4

tag: treatment

value: control


title: RN4220_empty

value: empty pRMC2


title: Dicer flox/- (mESCs)

city: Prague 4

first: Radek

last: Malik

address: Videnska 1083

department: Dep. of Epigenetics Regulations

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
The given adapters were trimmed, and the raw files were filtered by quality using the cutadapt tool with the following command line: cutadapt -m 15 -e 0.1 -o fastq -c -z -a adapter csfastq csqual
All fastq files were mapped in colorspace using the Shrimp short read aligner using following command line: shrimp -o 4 --strata -N 1 -L genome.index.i input.file
The *.bed files were constructed using the bamToBed command from the bedtools toolkit.
Genome_build: NCBI37/mm9 (without the chromosome containing "random" in their names) + pCAG-EGFP_MosIR plasmid sequence (available upon request).
Supplementary_files_format_and_content: *.bed file format

organism: Mus musculus

source_name: cell line

growth_protocol:
3T3 cells were grown under standard tissue culture conditions in DMEM supplemented with 10% FCS.
Mouse embryonic stem cells were cultured on gelatin-coated plastic in 2i-LIF medium: Knockout D-MEM (Invitrogen) containing 15% FCS (Sigma), 1× NEAA, 1 mM sodium pyruvate, 2 mM L-glutamine, 50 µM 2-mercaptoethanol, supplemented with mouse LIF (1,000 U/mL), 3μM CHIR99021, and 1 μM PD0325901 (Sellect Chemicals).

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

treatment_protocol:
NIH3T3 were co-transfected with pCAG-EGFP_MosIR and pcDNA4-DicerS-myc-His or pcDNA4-DicerS-myc-His (1.5 µg each per well in 6 well-plate). Cells were processed 48 hours post-transfection.
Mouse embryonic stem cell lines were transfected with pCAG-EGFP_MosIR plasmid (3 µg per well in 6 well-plate). Cells were processed 48 hours post-transfection.

tag: cell line

value: Dicer flox/- mouse embryonic stem cells

tag: passages


title: Dicer -/- mESCs, clone O4 transfected with pCAG-EGFP_MosIR expressing long hairpin derived from Mos gene

value: Dicer -/- mouse embryonic stem cells

tag: transfected plasmid


title: MHY200_30min

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

library_source: genomic

data_processing:
Sequence reads were mapped to the S. cerevisiae reference genome.
Sequence reads mapping to a single genomic location were summed in 1 kb bins. Windows where fewer than 250 reads were mapped in either sample were excluded.
Normalised copy numbers were generated by dividing the sequence read counts from the replicating sample by counts from the non-replicating cdc7 arrested) sample for each strain.
The resulting absolute ratios reflect the read numbers; therefore data was normalized to the read number in the two samples to give a genome-wide average of 1.
Finally the ratios were normalised to the FACS data to correct for the proportion of the was through S phase.
Genome_build: sacCer1
Supplementary_files_format_and_content: Wig file containing normalised replication profile.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Genomic DNA from S phase cells

extract_protocol:
DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to SOLiD instructions.

tag: strain

tag: relevant genotype

tag: growth protocol

value: Cells were released from a cdc7 arrest in rich media and a sample taken after 30 min.


title: MHY200_40min

value: Cells were released from a cdc7 arrest in rich media and a sample taken after 40 min.


title: Dicer -/- mESCs transfected with pCAG-EGFP_MosIR expressing long hairpin derived from Mos gene


title: MHY200_25min

value: Cells were released from a cdc7 arrest in rich media and a sample taken after 25 min.


title: eye-antenna_disc_faire

city: Chapel Hill

first: Daniel

middle: J

last: McKay

state: NC

address: 3344 Genome Sciences Building

department: Biology, Genetics

institute: The University of North Carolina at Chapel Hill

description:
FAIRE-seq
eye-antenna_disc_faire_rep1: CACGTCG
eye-antenna_disc_faire_rep2: GTTAATC
eye-antenna_disc_faire_rep3: ACAGTTG

data_processing:
Library strategy: FAIRE-Seq
Basecalls performed with CASAVA version 1.7.
FAIRE-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq HiSeq 2000 reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal Index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq signal files were generated by extending each read to a total of 110bp, and the number of reads overlapping each base in the genome was counted.
FAIRE data were normalized by subtracting Input signal from FAIRE at each base, and z-scores were generated using the mean and standard deviation for each chromosome arm.
FAIRE peaks were called using MACS2 with Input as control, a shift size of 125bp, and a q-value cutoff of 1.00e-2.
RNA-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
RNA-seq HiSeq 2000 reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
Genome_build: dm3
Supplementary_files_format_and_content: FAIRE processed data files are in wig format, and contain Input-subtracted FAIRE z-scores, smoothed with a 200bp sliding window average and 10bp step size.
Supplementary_files_format_and_content: RNA processed data files are matrices of gene names with their associated FPKM values calculated with Cuffdiff from the Tophat-aligned reads and using a RefSeq genome annotation file.

organism: Drosophila melanogaster

source_name: 3rd instar larval imaginal disc

growth_protocol: Bottles were flipped every 12 hours, and aged at 25C until the designated time.

extract_protocol:
Nuclei were pelleted, resuspended in FAIRE lysis buffer, and subjected to bead beating with 2mm tungsten beads. Chromatin was sonicated to a size range of 500bp-2kb, and phenol-chloroform extracted.
1-100ng DNA was prepared for sequencing on an Illumina GAII or HiSeq 2000 machine at the UNC High-Throughput Sequencing Facility.

treatment_protocol: Staged samples were fixed for 10 minutes at 25C, quenched with glycine, washed with Buffer A at 4C, Dounce homogenized in Buffer A, and filtered through 60uM Nitex.

value: y;cn,bw,sp

tag: developmental stage

value: 3rd instar larvae

tag: tissue

value: eye-antennal disc


title: larval_cns_faire

description:
FAIRE-seq
larval_cns_faire_rep1: AGATGGT
larval_cns_faire_rep2: GATCTTG
larval_cns_faire_rep3: TCAGGAC

source_name: 3rd instar larval central nervous system

value: central nervous system


title: pharate_haltere_faire

description:
FAIRE-seq
pharate_haltere_faire_rep1
pharate_haltere_faire_rep2

data_processing:
Basecalls performed with CASAVA version 1.7
FAIRE-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq HiSeq reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal Index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq signal files were generated by extending each read to a total of 110bp, and the number of reads overlapping each base in the genome was counted.
FAIRE data were normalized by subtracting Input signal from FAIRE at each base, and z-scores were generated using the mean and standard deviation for each chromosome arm.
FAIRE peaks were called using MACS2 with Input as control, a shift size of 125bp, and a q-value cutoff of 1.00e-2.
RNA-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
RNA-seq HiSeq reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
Genome_build: dm3
Supplementary_files_format_and_content: FAIRE processed data files are in wig format, and contain Input-subtracted FAIRE z-scores, smoothed with a 200bp sliding window average and 10bp step size.
Supplementary_files_format_and_content: RNA processed data files are matrices of gene names with their associated FPKM values calculated with Cuffdiff from the Tophat-aligned reads and using a RefSeq genome annotation file.

source_name: pharate appendage

value: stage P14 pharate adult

value: pharate haltere


title: pharate_wing_faire

description:
FAIRE-seq
pharate_wing_faire_rep1
pharate_wing_faire_rep2

value: pharate wing


title: MHY200_15min

value: Cells were released from a cdc7 arrest in rich media and a sample taken after 15 min.


title: MHY200_20min

value: Cells were released from a cdc7 arrest in rich media and a sample taken after 20 min.


title: pharate_T3leg_faire

description:
FAIRE-seq
pharate_T3leg_faire_rep1
pharate_T3leg_faire_rep2

value: T3 pharate leg


title: wt_40min


title: MHY200_cdc7

source_name: Genomic DNA from arrested cells

value: Cells were released from alpha factor into a cdc7 temperature arrest.


title: wt_30min


title: wt_35min

value: Cells were released from a cdc7 arrest in rich media and a sample taken after 35 min.


title: wt_25min


title: wt_20min


title: wt_15min


title: wt_alpha

value: Cells were grown to early-log phase in rich medium and then arrested with alpha factor.


title: MHY200_35min


title: C9 52i

city: Los Angeles

first: Robert

last: Baloh

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description:
Sample 8
mRNA profiling

data_processing:
Sequences were mapped to hg19 using Tophat
BAM files were imported into Partek software, and RPKM values calculated for each gene using RefSeq 10-16-2012 annotation
Genome_build: hg19
Supplementary_files_format_and_content: Text file containing abundance measurements (RPKM values) for each annotated gene

organism: Homo sapiens

source_name: iPSC derived motor neuron culture

extract_protocol:
iPSCs were differentiated into motor neurons, and RNA collected at 7 weeks after differentiation and prepared for sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols
Samples were indexed and sequenced together in two lanes of an Illumina HiSeq.  The two fastq files represent the same sample sequenced in the two different lanes

tag: disease state

value: ALS

tag: cell type

value: iPSC derived motor neuron culture

tag: barcode

value: TACTCTA


title: C9 30i

description:
Sample 7
mRNA profiling

value: CTTGGAA


title: C9 29i

description:
Sample 6
mRNA profiling

value: ATCGAGC


title: C9 28i

description:
Sample 5
mRNA profiling

value: CACCTCC


title: Control 83i

description:
Sample 4
mRNA profiling

value: Normal control

value: ATGACAG


title: wing_disc_faire

description:
FAIRE-seq
wing_disc_faire_rep1
wing_disc_faire_rep2
wing_disc_faire_rep3

value: y;cn,bw,sp

value: 3rd instar larvae

value: wing disc


title: genomic_input_ycnbwsp

description:
Input
genomic_input_ycnbwsp

source_name: adult female virgins

extract_protocol: 1-100ng DNA was prepared for sequencing on an Illumina GAII or HiSeq 2000 machine at the UNC High-Throughput Sequencing Facility.

value: adult

value: whole adult


title: Control 14i

description:
Sample 3
mRNA profiling

value: GCTTAGA


title: MHY200_alpha


title: T3leg_disc_faire

description:
FAIRE-seq
T3leg_disc_faire_rep1
T3leg_disc_faire_rep2
T3leg_disc_faire_rep3

value: T3 leg disc


title: Control 00i

description:
Sample 1
mRNA profiling

value: TGAGGTT


title: Totals from lysates treated like PAR-CLIP samples

city: Durham

first: Matthew

middle: Burk

last: Friedersdorf

address: 207 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

description:
Total RNA from lysates of cells grown with 4SU, crosslinked at UV 365nm, RNase T1 digested, proteinase K digested, and depleted for rRNA using RiboZero
Illumina SE-50bp; Tru-seq small RNA

data_processing:
adapter clipping: fastx_clipper -a TCGTATGCCGTCTTCTGCTTG -1 13 (Fastx toolkit)
genome alignment: bowtie hg19 -v 2 -m 10 --all --best --strata
PARalyzer (ini file): BANDWIDTH=3  CONVERSION=T>C  MINIMUM_READ_COUNT_PER_GROUP=1  MINIMUM_READ_COUNT_PER_CLUSTER=5  MINIMUM_READ_COUNT_FOR_KDE=5  MINIMUM_CLUSTER_SIZE=5  MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=1  MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=1  MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=5  MINIMUM_READ_LENGTH=1  MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=0    EXTEND_BY_READ
Note: processed files still contain regions mapping to repetitive sequences, although most downstream analysis will require removal of these sequences
Genome_build: hg19
Supplementary_files_format_and_content: csv; group (Chromosome,Strand,Start,End,GroupID,GroupSequence,ReadCount,ConversionLocationCount,ConversionEventCount,annotation source,TranscriptLocation,TranscriptID,GeneName  ); cluster (Chromosome,Strand,Start,End,ClusterID,ClusterSequence,ReadCount,ModeLocation,ModeScore,ConversionLocationCount,ConversionEventCount,NonConversionEventCount,annotation source,TranscriptLocation,TranscriptID,GeneName)

source_name: tissue culture cell line

extract_protocol:
Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jr., Jungkamp AC, Munschauer M et al: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141(1):129-141.
Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, Tuschl T: Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 2008, 44(1):3-12.

tag: crosslinker & wavelength

value: 4SU & UV 365nm

tag: rnase

value: RNase T1

tag: immunoprecipitated protein

tag: antibody


title: PAR-CLIP HuR, replicate1

description:
PAR-CLIP
Illumina SE-50bp; Tru-seq small RNA

growth_protocol: Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jr., Jungkamp AC, Munschauer M et al: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141(1):129-141.

value: HuR

value: FLAG M2


title: e16-18hr_faire

description:
FAIRE-seq
e16-18hr_faire_rep1
e16-18hr_faire_rep2

source_name: 16-18 hour embryos

growth_protocol: Following a pre-clearing step, embryos were collected for 2 hours and aged at 25C until the designated time.

value: OregonR

value: 16-18 hours after egg laying

value: whole embryo


title: e6-8hr_faire

description:
FAIRE-seq
e6-8hr_faire_rep1
e6-8hr_faire_rep2

source_name: 6-8 hour embryos

value: 6-8 hours after egg laying


title: PAR-CLIP background, ~45KDa; G45

treatment_protocol: Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jr., Jungkamp AC, Munschauer M et al: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141(1):129-141.

value: GFP


title: HeLa_NO_SSase_plusP_rep1

status: Public on Nov 06 2013

city: Philadelphia

first: Ian

middle: M

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

department: Biology

institute: University of Pennsylvania

description: Processed data file: HeLa_NO_SSase.CSAR_PPS_FDR05.bed

data_processing:
Library strategy: Protein interaction profile sequencing (PIP-seq)
Basecalls performed with Bustard 1.13.48.
3' adapter sequences were trimmed using cutadapt (version 0.9.5 with parameters -e 0.06 -O 6 -m 14).
Trimmed reads were aligned to the human genome (hg19) using Tophat (version 2.0.9 with parameters --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --transcriptome-max-hits 10 --no-coverage-search --no-novel-juncs).
Protein-protected sites were identified using a modified version of the CSAR software package (Muino et al. 2011). Specifically, read coverages were calculated for each base position in the genome and a Poisson test was used to compute an enrichment score for 'protected' versus 'unprotected' libraries. PPSs were then called as described (Muino et al. 2011) with an FDR of 5%.
Genome_build: GRCh37
Supplementary_files_format_and_content: BED format of protein protected sites (PPSs).

source_name: HeLa cells, no crosslinker, ssRNase, protein bound

growth_protocol: For these experiments, HeLa cells were seeded in 15 cm flasks, grown to 90% confluency in DMEM media (Life Technologies, San Diego, CA) supplemented with L-glutamine, 4.5 g/L D-Glucose, 10% FBS serum (Atlanta Biologics, Atlanta, GA), and Pen/Strep (Fisher Scientific, Waltham, MA).

extract_protocol:
We lysed the cell pellets using RIP buffer (25 mM Tris-HCl, pH = 7.4; 150 mM KCl, 5 mM EDTA, pH = 7.5; 0.5% NP40; 10 mM DTT; 1 tablet protease inhbitors/10mL) and manual grinding. The resulting cell lysate was treated with RNase-free DNase (Qiagen; Valencia, CA). Subsequently, these DNA-depleted lysates were treated with either a single-stranded RNase (ssRNase) (RNaseONE (Promega; Madison, WI)) or double-stranded RNase (dsRNase) (RNaseV1 (Ambion; Austin, TX)) as previously described ((Zheng et al. 2010; Li et al. 2011), see Fig. 1A for a schematic description). Proteins were then denatured and digested by treatment with 1% SDS and 0.1mg/ml Proteinase K (Roche; Basel, Switzerland). It is worth noting for clarity that we had two cell lysates for these experiments: one treated with the ssRNase and the other with dsRNase. For formaldehyde cross-linking experiments, Proteinase digestion was followed by a 2-hour incubation at 65°C to reverse the crosslinks, whereas for UV cross-linking experiments, RNA was liberated from protein by retreating the lysates with 1% SDS and 1 mg/ml Proteinase K for 30 minutes. To determine whether nuclease-resistant regions in RNAs are due to protein binding or specific secondary structures, we also determined the digestion patterns of ds- and ssRNases in the absence of bound proteins. To do this, we performed the identical treatments as described directly above except that the cross-linked cellular lysates were treated with 1% SDS and 0.1 mg/ml Proteinase K (Roche; Basel, Switzerland) and ethanol precipitated prior to being treated with the two RNases. In this way, the SDS and Proteinase K solubilized and digested the proteins allowing us to deduce protein-protected sites within all detectable RNAs in the cells of interest (see Fig. 1 for schematic). The digested RNA was then isolated using the Qiagen miRNeasy RNA isolation kit following the included protocol (Qiagen; Valencia, CA).
Purified RNA was used as the substrate for strand-specific sequencing library preparation (TruSeq small RNA sequencing kit [illumina, Valencia, CA]), as previously described (Zheng et al. 2010; Li et al. 2011), with the exception that we also include DSN library normalization per manufacturer instructions (Illumina; San Diego, CA).

treatment_protocol:
For formaldehyde crosslinking, 37% formaldehyde solution (Sigma, St. Louis, MO) was added drop-wise with mixing directly to cell culture dishes to a final concentration of 1% and incubated at room temperature for 10 minutes. Next, 1M glycine (Sigma, St. Louis, MO) was added to a final concentration of 125 mM and incubated for an additional 5 minutes with mixing. Then, cells were washed twice with ice cold PBS and collected. Finally, cells were pelleted and frozen until the PIP-seq digestions were performed.
For UV cross-linking experiments, cells were washed twice with ice cold PBS and resuspended in 5 ml of PBS. Cell culture dishes were placed in a UV Stratalinker 2400 (Agilent Technologies, New Castle, DE) with the lid removed and irradiated with UV-C (254 nm) once with 400 mj/cm2. Cells were collected by scraping, pelleted and then frozen until use.

value: HeLa

tag: crosslinker

value: ssRNase (RNase ONE)

tag: protein-bound

value: yes


title: PAR-CLIP background, ~20KDa; G20

tag: cell line


title: wt_cdc7

value: Cells were released from alpha factor into a cdc7 temperature arrest.


title: PAR-CLIP background, ~35KDa; G35


title: HeLa_NO_SSase_minusP_rep1

source_name: HeLa cells, no crosslinker, ssRNase, not protein bound

value: no


title: HeLa_NO_DSase_minusP_rep1

description: Processed data file: HeLa_NO_DSase.CSAR_PPS_FDR05.bed

source_name: HeLa cells, no crosslinker, dsRNase, not protein bound

value: dsRNase (RNase V1)


title: HeLa_NO_DSase_plusP_rep1

source_name: HeLa cells, no crosslinker, dsRNase, protein bound


title: HeLa_UV_SSase_minusP_rep1

description: Processed data file: HeLa_UV_SSase_rep1.CSAR_PPS_FDR05.bed

source_name: HeLa cells, UV, ssRNase, not protein bound

value: UV


title: HeLa_UV_SSase_plusP_rep1

source_name: HeLa cells, UV, ssRNase, protein bound


title: HeLa_UV_SSase_plusP_rep2

description: Processed data file: HeLa_UV_SSase_rep2.CSAR_PPS_FDR05.bed


title: HeLa_UV_SSase_minusP_rep2


title: Control 03i

description:
Sample 2
mRNA profiling

value: Normal control

value: iPSC derived motor neuron culture

value: AGACTGA


title: haltere_disc_faire

description:
FAIRE-seq
haltere_disc_faire_rep1
haltere_disc_faire_rep2
haltere_disc_faire_rep3

value: y;cn,bw,sp

value: 3rd instar larvae

value: haltere disc


title: HeLa_UV_DSase_plusP_rep2

description: Processed data file: HeLa_UV_DSase_rep2.CSAR_PPS_FDR05.bed

source_name: HeLa cells, UV, dsRNase, protein bound


title: HeLa_UV_DSase_minusP_rep1

description: Processed data file: HeLa_UV_DSase_rep1.CSAR_PPS_FDR05.bed

source_name: HeLa cells, UV, dsRNase, not protein bound


title: e2-4hr_faire

description:
FAIRE-seq
e2-4hr_faire_rep1
e2-4hr_faire_rep2

source_name: 2-4 hour embryos

value: OregonR

value: 2-4 hours after egg laying


title: HeLa_UV_DSase_plusP_rep1


title: HeLa_Form_SSase_minusP_rep3

description: Processed data file: HeLa_Form_SSase_rep3.CSAR_PPS_FDR05.bed

source_name: HeLa cells, formaldehyde, ssRNase, not protein bound

value: formaldehyde


title: HeLa_Form_SSase_minusP_rep2

description: Processed data file: HeLa_Form_SSase_rep2.CSAR_PPS_FDR05.bed


title: HeLa_Form_SSase_minusP_rep1

description: Processed data file: HeLa_Form_SSase_rep1.CSAR_PPS_FDR05.bed


title: PAR-CLIP HuR, replicate2

value: 4SU & UV 365nm

value: RNase T1

value: HuR

value: FLAG M2


title: HeLa_Form_SSase_plusP_rep2

source_name: HeLa cells, formaldehyde, ssRNase, protein bound

value: HeLa

value: ssRNase (RNase ONE)

value: yes


title: HeLa_Form_SSase_plusP_rep3


title: HeLa_UV_DSase_minusP_rep2

value: UV

value: dsRNase (RNase V1)

value: no


title: HeLa_Form_DSase_minusP_rep3

description: Processed data file: HeLa_Form_DSase_rep3.CSAR_PPS_FDR05.bed

source_name: HeLa cells, formaldehyde, dsRNase, not protein bound


title: HeLa_Form_SSase_plusP_rep1


title: HeLa_Form_DSase_minusP_rep2

description: Processed data file: HeLa_Form_DSase_rep2.CSAR_PPS_FDR05.bed


title: HeLa_Form_DSase_minusP_rep1

description: Processed data file: HeLa_Form_DSase_rep1.CSAR_PPS_FDR05.bed


title: HeLa_Form_DSase_plusP_rep2

source_name: HeLa cells, formaldehyde, dsRNase, protein bound


title: HeLa_Form_DSase_plusP_rep3


title: 09H030

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8
Sequenced reads were mapped to the reference genome using CASAVA 1.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: acute lymphoblastic leukemia

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Sample Preparation (Illumina)

value: bone marrow


title: 08H028

value: blood


title: 08H125


title: 11H099


title: HeLa_Form_DSase_plusP_rep1


title: 05H125


title: 03H096


title: 05H129


title: 03H078


title: 05H183


title: ED39

data_processing:
Basecalls performed using CASAVA 1.8.2.
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome (hg19) using CASAVA 1.8.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: cord blood cells

growth_protocol: Primary cells.

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106).
TruSeq RNA Sample Preparation (Illumina).

treatment_protocol: Sorting by FACS of CD34+ and CD34+CD45RA- cells.

value: peri-natal

value: umbilical cord blood

tag: sorted cell type


title: 05H080


title: ED38


title: ED32


title: ED31


title: ED37


title: ED26


title: ED25


title: ED23


title: ED16


title: ED20


title: ED15


title: ED14


title: ED11


title: 07H033


title: ED06


title: 0.5U Mnase digest input

city: Madison

first: Tao

last: Zhang

state: WI

address: 1575 Linden Dr.

department: Horticulture

institute: University of Wisconsin Madison

description: Sample 2

data_processing:
DNA fragments were mapped to rice genome (TIGR7/IRGSP1) (Kawahara et al., 2013; Sakai et al., 2013), with Bowtie (Langmead et al., 2009) reporting non-mismatches and uniquely mapped sites.
The centers of CENH3 nucleosomes were identified by nucleR (Flores and Orozco, 2011).
Genome_build: TIGR7
Supplementary_files_format_and_content: The wig files report nucleR's score. The peak sites are the center of CENH3 nucleosomes.

organism: Oryza sativa

source_name: leaf DNA, 0.5U Mnase digest input

growth_protocol: Rice cultivar “Nipponbare” seeds were germinated at room temperature for three days. Germinated seeds were then sowed in soil to continue to grow in the greenhouse. Two-week old seedlings were collected for nuclei and DNA isolation.

extract_protocol:
The collected seedlings were grounded into fine powder in liquid nitrogen. The ChIP procedure, including nuclei isolation, MNase digestion, immunoprecipitation using anti-cenH3 antibodies and recovery of ChIPed DNA for development of ChIP-seq libraries, was carried out by following the published protocols (Zhang et al., 2012)
ChIPed DNA and input DNA corresponding to 0.5 U and 2.5 U MNase digested chromatins were used for customized ChIP-seq library development following the published protocols (Henikoff et al., 2011), which can recover insert sizes down to 20 bp.

value: two-week old seedling

value: leaf

tag: cultivar

value: Nipponbare

tag: mnase digestion

value: 0.5U Mnase

tag: chip antibody


title: s_8

city: Hanover

first: Gavin

middle: D

last: Grant

state: NH

address: 7400 Remsen

department: Genetics

institute: Geisel School of Medicine

description: Sample 2

data_processing:
Reads were aligned to hg19 using Bowtie software (v 0.12.7)
Enriched peaks were identified independently in each dataset using MACS (v. 1.4.1)
Genome_build: HG19
Supplementary_files_format_and_content: s_7_peaks.bed.gz contains the peaks called by MACS for sample s_7
Supplementary_files_format_and_content: s_8_peaks.bed.gz contains the peaks called by MACS for sample s_8

source_name: HeLa S3_FOXM1 ChIP

growth_protocol: HeLa cells were passaged in a 37C, humidity controlled, CO2 equilibrated incubator in DMEM (Life Technologies) media containing 10% FBS (Life Technologies), and 1% Penn-Strep (Life Technologies)

extract_protocol:
HeLa cells were fixed with 1% formaldehyde before the DNA was sonicated to a fragment length of 200-600bp with a Bioruptor® (Diagenode, Sparta, NJ).  Antibodies were bound to a mix of Protein A and Protein G Dynabeads® (Life Technologies, Grand Island, NY) before an 18 hour incubation at 4°C with the fragmented DNA. DNA was washed and crosslinks reversed before purification with a QIAquick™ PCR purification kit (QIAGEN, Valencia, CA).  DNA concentrations were measured using Quant-iT™ PicoGreen® (Life Technologies, Grand Island, NY).
A library was constructed from the bound fragments per manufacturer’s protocols and the DNA fragments from each independent ChIP were sequenced independently at the UNC High Throughput Sequencing Facility using an Illumina Genome Analyzer II.

value: HeLa S3

value: epithelial

value: FOXM1 Antibody (C-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: 2.5U Mnase digest input

description: Sample 4

source_name: leaf DNA, 2.5U Mnase digest input

tag: developmental stage

tag: tissue

value: 2.5U Mnase


title: 0.5U Mnase digest anti-CENH3

description: Sample 1

source_name: leaf DNA, 0.5U Mnase digest anti-CENH3

value: anti-CENH3 (custom Ab; Nagaki, 2004, Nature Genetics)


title: 2.5U Mnase digest anti-CENH3

description: Sample 3

source_name: leaf DNA, 2.5U Mnase digest anti-CENH3


title: ED35


title: Mnase digest Naked DNA

description: Sample 6

source_name: leaf DNA, Mnase digest Naked DNA

value: 0.001U Mnase (digestion of naked DNA)


title: s_7

description: Sample 1

tag: cell type


title: 4.0U Mnase digest anti-CENH3

description: Sample 5

source_name: leaf DNA, 4.0U Mnase digest anti-CENH3

value: 4.0U Mnase


title: p300 Craniofacial ChIP-seq

city: Berkeley

first: Alex

middle: S

last: Nord

address: 1 Cyclotron Road, Mail Stop 84-171

department: Genomics Divsion

institute: Lawrence Berkeley National Laboratory

data_processing:
Reads mapped to the mouse genome (mm9) using BWA (bwa aln -t 5 -l 25)
Peaks called using MACS v1.4 (macs14 --bw=300 --mfold=10,30 --nolambda --nomodel --shiftsize=150 -p 1x10-4)
Peaks filtered to remove regions where significant proportion of reads originated in repetitive sequence
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include peaks in bed format and coverage in wig format

source_name: craniofacial tissue

extract_protocol:
Tissue dissected from e11.5 CD1 mouse embryos and crosslinked with 1% formaldehyde. Lysates were clarified from sonicated nuclei and p300-DNA complexes were isolated with antibody.
Illumina TruSeq Kit protocol

value: craniofacial tissue

tag: strain


title: 32g58 Control, replicate 1

city: Brookings

first: Joy

last: Scaria

state: SD

department: Veterinary and Biomedical Sciences

institute: South Dakota State University

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of the raw sequence reads was checked using the FastQC program (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc). The processed reads were then aligned using Bowtie version 0.12.7  to the corresponding C. difficile reference genome. Read alignments with mapping quality score (MAPQ) < 10 were removed.
Cufflinks software package version 1.3.1  was used to assemble transcripts and estimate the relative abundances of the transcripts. Transcript expression levels are estimated as Fragments Per Kilobase per Million mapped reads (FPKM). Cuffdiff, a component of Cufflinks was used to calculate transcript expression levels. When compared to control condition, genes with log2 ratio ≥ 1.5 and FDR- adjusted p value less than or equal to 0.05 were considered as differentially expressed.
Genome_build: ASM920v1, ASM8522v1, ASM2710v1, ASM15266v1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Clostridioides difficile

source_name: 32g58_Brain heart infusion broth

growth_protocol: Spores of C. difficile strains CD630, CD196, QCD_32g58 and R20291 were streaked on brain-heart infusion (BHI) agar plates containing 0.1% L-cysteine and taurocholate. The plates were incubated overnight at 37°C. Single colonies from these plates were then used inoculate pre-reduced BHI broth and were incubated at 37°C overnight. Fresh BHI broth was then inoculated by transferring 1% overnight culture. Cultures were incubated at 37°C until the OD600 reached between 0.4 - 0.5.

extract_protocol:
Groth was arrested by addition of twice volume of RNAprotect bacteria reagent. Cells were collected by centrifugation at 2,000 x g for 10 minutes.  RNA was isolated using RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bacteria were then collected by centrifugation at 2,000 x g for 5 minutes. These cells were then shifted to two physiologically relevant in vitro conditions. In the first condition, cells were subjected to nutrient change by shifting to an equal volume of Basal defined medium (BDM) with supplementation of 0.5% sucrose. In the second condition, cells were subjected to osmotic shock by shifting to an equal volume of BHI supplemented with 1.5% NaCl. The same  number of cells was transferred to fresh BHI as the control group.

tag: growth/treatment condition

value: grown to mid log phase


title: 32g58 Osmotic shock, replicate 1

source_name: 32g58_Brain heart infusion broth+1.5 % NaCl

value: exposed to Brain heart infusion broth supplimented with 1.5% NaCl for 1h


title: 32g58 Nutrient shift, replicate 2

source_name: 32g58_Basal defined medium

value: exposed to basal defined medium  for 1h


title: 32g58 Control, replicate 2


title: 32g58 Osmotic shock, replicate 2


title: R20291 Nutrient shift, replicate 1

source_name: R20291_Basal defined medium

value: exposed to basal defined medium for 1h


title: 32g58 Nutrient shift, replicate 1


title: R20291 Osmotic shock, replicate 2

source_name: R20291_Brain heart infusion broth+1.5 % NaCl


title: ED18

value: peri-natal

value: umbilical cord blood


title: R20291 Control, replicate 2

source_name: R20291_Brain heart infusion broth


title: R20291 Osmotic shock, replicate 1


title: ED07


title: CD196 Nutrient shift, replicate 2

source_name: 196_Basal defined medium


title: R20291 Control, replicate 1


title: CD196 Osmotic shock, replicate 2

source_name: 196_Brain heart infusion broth+1.5 % NaCl


title: CD196 Osmotic shock, replicate 1


title: CD196 Control, replicate 2

source_name: 196_Brain heart infusion broth


title: CD196 Control, replicate 1


title: CD630 Nutrient shift, replicate 2

source_name: 630_Basal defined medium


title: CD630 Nutrient shift, replicate 1


title: Nr32 DOG 20day rep1

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina Casava1.7 software used for extraction of FASTQ files
FASTQ files were mapped using TopHat (v1.4.1, parameters: --butterfly-search -g 1) vs. the C. elegans genome assembly WS220 (Ensembl release 66)
Gene counts were obtained using the Python package HTSeq and the respective Ensembl annotation GTF file (parameters: –stranded=no --idattr=gene_id --mode=union)
HTSeq result files were processed using the R programming language and RPKM values were calculated
Genome_build: WS220 (ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic/c_elegans.WS220.genomic.fa.gz)
Supplementary_files_format_and_content: raw counts and RPKM values for each sample

organism: Caenorhabditis elegans

source_name: total RNA from whole animals

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at −80°C until use.
Total RNA was inspected for degradation using Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). For library preparation an amount of 2μg of total RNA per sample was processed using Illumina's TruSeq™ RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer's instruction. Each library includes its own index sequence.

treatment_protocol: Treatment of C. elegans was carried out on NGM agar plates containing 5 mM Of 2-deoxy-D-glucose. All agar plates were prepared from the same batch of NGM agar, whereas treatment plates were supplemented with the respective compound.

value: Adult (20 days after L4)

tag: age

value: 20 days after L4

value: N2 (var. Bristol)

tag: agent

value: 5mM DOG


title: Nr27 DOG 10day rep3

value: Adult (10 days after L4)

value: 10 days after L4


title: Nr33 DOG 20day rep2


title: Nr26 DOG 10day rep2


title: CD630 Osmotic shock, replicate 2

source_name: 630_Brain heart infusion broth+1.5 % NaCl


title: CD630 Osmotic shock, replicate 1


title: Nr18 DOG 5day rep3

value: Adult (5 days after L4)

value: 5 days after L4


title: R20291 Nutrient shift, replicate 2


title: Nr16 DOG 5day rep1


title: Nr17 DOG 5day rep2


title: CD630 Control, replicate 1

source_name: 630_Brain heart infusion broth


title: Nr08 DOG 1day rep2

value: Adult (1 days after L4)

value: 1 days after L4


title: Nr07 DOG 1day rep1


title: CD196 Nutrient shift, replicate 1


title: Nr09 DOG 1day rep3


title: 03H005

source_name: acute lymphoblastic leukemia

value: blood


title: Saos-2 BrdU-Seq Input

status: Public on Nov 05 2013

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

data_processing:
Library strategy: BrdU-Seq
Reads were aligned to the human hg19 genome assembly using bowtie-0.12.7 with parameters -r --offrate 6 -m 1 --best --strata -t -v 2
peaks were called based on the p value for Poisson distribution of enriched immunoprecipitated DNA relative to input. Significant BrdU peaks were defined as those windows with a p value<10e-4 and with two neighboring windows at the same significance. Significant H3K18ac peaks were defined as those windows with a p value<10e-3 and with two neighboring windows at the same significance.
Genome_build: hg19
Supplementary_files_format_and_content: bed and wig files

source_name: Saos-2 osteosarcoma

growth_protocol: Saos-2 Cells were cultured in DMEM (Cellgro) that was supplemented with 10% FBS (Hyclone) and 1X antibiotic (Gibco).  Cells were passaged every 2-3 days.

extract_protocol: BrdU-Seq: 4 µg of BrdU labelled DNA was heated in 0.1 M NaOH at 95°C for 5 min to remove RNA primers on nascent strand DNA. HCl was then added to neutralize the pH. TE buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA) was added to bring the total volume 500 µl. DNA was fragmented by sonication and denatured by heating at 95°C for 5 min. 0.1 volume of Adjusting buffer (110 mM sodium phosphate buffer, pH7.0, 1.54 M NaCl, 0.55% Triton X-100) was then added to DNA. DNA was subsequently incubated with 2 µg of BrdU antibody (BD Biosciences, 347580) and Dynabeads Protein G (Life Technologies). After immunoprecipitation, DNA was purified using phenol/chloroform extraction and ethanol precipitation. Double-stranded DNA was generated from both input and immunoprecipitated DNA by brief random priming with the Bioprime DNA Labeling System (Life Technologies) at 37 °C for 20 min. Sequencing libraries were prepared with Chip-Seq DNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

value: Osteosarcoma

tag: culture medium

value: DMEM supplemented with 10% FBS and 1X antibiotics

tag: antibody

tag: sirna treatment


title: Saos-2 BrdU-Seq

growth_protocol: Saos-2 cells were cultured in DMEM (Cellgro) that was supplemented with 10% FBS (Hyclone) and 1X antibiotic (Gibco).  Cells were passaged every 2-3 days.

value: BrdU (BD Biosciences, 347580)

tag: cell line


title: SMA_WM rep2

first: Zhenxi

state: PA

address: 415 Curie Blvd., 330 CRB

department: Biochemistry and Biophysics

institute: University of Pennsylvania School of Medicine

data_processing:
RNA-seq data were aligned to reference genome (UCSC, mm9) using Tophat by default parameters.
Uniquely mapped and properly paired alignments were kept for computing raw count and RPKM for each gene using BEDTools.
The analysis of differentially expressed genes between WT and SMA samples was performed by DESeq.
MISO was applied to the aligned RNA-seq data to identify alternative splicing events between WT and SMA samples.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM of each gene for each sample.

source_name: White matter glia

extract_protocol:
lumbar spinal cord was dissected, embedded in NEG 50 (Richard-Allan Scientific) on dry ice/ethanol mixture. Cross-sections of 8 μm thickness were prepared in a cryostat and transferred to PEN membrane slides (Zeiss). Slides were stained by Mayer’s hematoxylin (Sigma), using a LCM staining kit (Ambion). Laser-capture microdissection (LCM) was performed on a PALM microbeam UV laser microdissection system (Zeiss). Total RNA from LCM samples was purified by using RNeasy Plus Micro kit (Qiagen).
ds-cDNA was produced by using Ovation RNA-seq System V2 (NuGEN) and fragmented by a Covaris S-series System (Covaris). DNA fragments in 150-300 bp size range were recovered to construct sequencing library, using Encore NGS Library System I (NuGEN)

value: FVB/N

value: Lumbar segment spinal cord

tag: cell

value: White matter glia

value: Postnatal day 1

tag: genotype


title: WT_WM rep1

value: WT


title: SMA_WM rep1


title: WT_WM rep2


title: SMA_MNs rep1

source_name: Motor neurons

value: Ventral horn motor neurons


title: PIC 4

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

country: Australia

institute: The Australian National University

data_processing:
Basecalls performed using CASAVA version 1.2
Reads aligned to reference transcriptome with Bowtie v0.12.7
Counts per reference were summarised using in-house scripts
Genome_build: NCBI Transcriptome Shotgun Assembly Database numbers JR970414–JR999999 and JT000001–JT023377
Supplementary_files_format_and_content: Reference trancript name, TAB, count

organism: Acropora millepora

source_name: Branch

extract_protocol:
Trizol extraction of total RNA, Dynal beads extraction of messenger RNA
Illumina single end RNA-seq protocol carried out bt by GeneWorks Australia Pty Ltd

value: Adult

tag: immunogen treatment

value: PIC

tag: time after exposure

value: 1 hour


title: WT_MNs rep2


title: PIC 3


title: WT_MNs rep1


title: PIC 2


title: Nr25 DOG 10day rep1

value: Adult (10 days after L4)

value: 10 days after L4

value: N2 (var. Bristol)

value: 5mM DOG


title: PIC 1


title: MDP 1

value: MDP


title: Control 2

value: Sea water


title: Control 4


title: CD630 Control, replicate 2

value: grown to mid log phase


title: Control 3


title: 3KR_dex_SUMO_2_3_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: isogenic HEK293 cells were created by using the Flp-In System (Invitrogen)

data_processing:
Basecalls performed using CASAVA
FASTX-toolkit was used to trim the raw  reads to 40 bp and sequence duplicates were collapsed
the reads were aligned to human reference genome version hg19 by using Bowtie software version 0.12.9. with the command line: -e 70 -l 50 -n 1 -k 1 -m1 \ -t -p 12 -q -S --best
peaks were called using MACS program version 1.4.2. with the following setting: bandwidth (100 for GR; 200 for SUMO_2_3), mfold (10,30 for GR; 10,15 for SUMO_2_3), p-value cut-off (0.0001), Input as control for GR and IgG for SUMO_2_3
statistically significant peaks had tags (> 50), fold enrichment (> 8), false discovery rate (< 0.1) and peak had to be present in two biological replicates
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks from each immunoprecipitated sample: chr, start, end, length, summit, tags, -log10(p-value), fold enrichment, FDR(%)

source_name: Isogenic HEK293 Cells

growth_protocol: Isogenic HEK293 cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator

extract_protocol:
Lysates were clarified from sonicated nuclei and GR-DNA complexes were isolated with 1 µg of antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols, as utilized at the Gene Core in EMBL, Heidelberg, Germany

treatment_protocol: Isogenic HEK293 cells were seeded at 70 % confluence in 175 cm2 bottles and allowed to grow in steroid-depleted medium (2.5 %  charcoal stripped FBS in DMEM) 72 h and the cells were subsequently treated with 100 nM of dexamethasone for 1 h prior ChIP

value: Human Embryonal Kidney Cells

tag: chip antibody

value: SUMO-2/3 (MBL International, M114-3, lot # 23)

tag: stably expressing

value: SUMOylation-defective GR

tag: treatment

value: dexamethasone

tag: concentration

tag: time

value: 1 h


title: 3KR_dex_SUMO_2_3_rep1


title: Submerged

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
Illumina 1.3 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Reads per kilobase per million (RPKM) value was calculated for all the genes in each tissue sample
Genome_build: Porteresia Transcriptome Assembly (v1.0) available at http://nipgr.res.in/mjain.html?page=porteresia
Supplementary_files_format_and_content: tab delimited text files include RPKM values for each sample

organism: Oryza coarctata

source_name: Mature plant

growth_protocol: Plants were collected from natural conditions

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacture’s protocol

treatment_protocol: We collected different tissue samples after various treatments (control, in water; salt450, in 450 mM sodium chloride solution; salt700, in 700 mM sodium chloride solution; submergence, submerged in water; salt+submergence, submerged in 450 mM sodium chloride solution).

tag: tissue

value: Mature plant

tag: treated in

value: submerged in water


title: wt_dex_SUMO_2_3_rep1

value: wild-type GR


title: SMA_MNs rep2

tag: strain

value: FVB/N

value: Lumbar segment spinal cord

value: Ventral horn motor neurons

tag: age

value: Postnatal day 1


title: Salt450+Submerged

value: submerged in 450 mM sodium chloride solution


title: wt_dex_SUMO_2_3_rep2


title: Salt450

value: 450 mM sodium chloride solution


title: Control

value: water (control)


title: 3KR_dex_GR_rep1

value: GR (Santa Cruz, sc-1003, lot # D1812)


title: FRT_dex_GR

description: isogenic HEK293 control FRT cells were created by using the Flp-In System (Invitrogen)


title: wt_dex_GR_rep2


title: wt_dex_GR_rep1


title: MDP 2

tag: developmental stage

value: Adult

value: MDP

value: 1 hour


title: H1 ChIP-Seq Input

data_processing:
Reads were aligned to the human hg19 genome assembly using bowtie-0.12.7 with parameters -r --offrate 6 -m 1 --best --strata -t -v 2
peaks were called based on the p value for Poisson distribution of enriched immunoprecipitated DNA relative to input. Significant BrdU peaks were defined as those windows with a p value<10e-4 and with two neighboring windows at the same significance. Significant H3K18ac peaks were defined as those windows with a p value<10e-3 and with two neighboring windows at the same significance.
Genome_build: hg19
Supplementary_files_format_and_content: bed and wig files

source_name: H1 embryonic stem cells

growth_protocol: H1 embryonic stem cells were cultured in mTESR1 medium. Cells were passaged every 5-6 days.

extract_protocol: H3K18ac ChIP: 20,000,000 Cells were resuspended in 450 ul of lysis buffer and incubated for 10 min on ice and immediately sonicated using Misonix cup-horn sonicator. 100 ul of the lysate (corresponding to 5,000,000 cells) were used for each immunoprecipitation with H3K18ac antibody; 10 ul of the lysate was used as input. After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min at 37°C, proteinase K for 2 h at 56°C. DNA was subsequently purified using phenol/chloroform extraction and ethanol precipitation. DNA concentration was measured using Qubit (Life Technologies).  Sequencing libraries were prepared with Ovation Ultralow DR Systems (NuGEN) according to the manufacturer's instructions.

tag: cell type

value: Embryonic stem cells

tag: culture medium

value: mTESR1 (STEMCELL Technologies)

tag: passage

value: Between 35 to 45

tag: antibody


title: MDP 3


title: IMR90 ChIP-Seq Input

source_name: IMR90 fibroblasts

growth_protocol: IMR90 cells were cultured in DMEM (Cellgro) that was supplemented with 10% FBS (Hyclone) and 1X antibiotic (Gibco).  Cells were passaged every 3 days.

value: Primary lung fibroblasts

value: DMEM supplemented with 10% FBS and 1X antibiotics

value: Between 7 to 12

tag: cell line

tag: sirna treatment


title: Salt700

value: Mature plant

value: 700 mM sodium chloride solution


title: IMR90 H3K18ac ChIP-Seq

value: Custom 814 H3K18ac


title: H1 EP300_CREBBP Knockdown BrdU-Seq Input

treatment_protocol: siRNA treatment: EP300 and CREBBP siRNA (Thermo Scientific) was mixed with DharmaFECT 1 (Thermo Scientific) in Opti-MEM (Life Technologies). After incubation for 20 minutes at room temperature, the siRNA-DharmaFECT 1 complex was added to 6-well plates that were pre-coated with Matrigel (BD Biosciences). 300,000 of hESCs in single cell suspension were added to each well and mixed with transfection reagents. HA 1077 (EMD Millipore) was added to culture media to final concentration 10 µM. Same amount of non-targeting siRNA was used as control. Cells were collected at 72 hr post-transfection.

value: EP300 and CREBBP


title: 2 dpi MGPC, apobec2a,2b Mo_Sample 12847

city: Ann Arbor

first: Ana

middle: Rodrigues

state: MI

address: 100 Washtenaw Avenue

department: Computational Medicine & Bioinformatics

institute: University of Michigan

description:
Bisulfite treated, MspI digestion
apobec2a,2b morpholino was delivered at the time of injury (6 x 0.7 μl of 0.25mM morpholino injections per eye) by using a Hamilton syringe. Morpholino delivery to cells was facilitated by electroporation. 6 additional lesions per eye were performed following electroporation.

data_processing:
Basecalls performed with CASAVA version 1.8.2
Sequences were trimmed to remove PCR primers, adapter sequences and low-quality base calls (score <20) with TRIM_GALORE version 0.2.1
Reads (100b paired for MG and 4dpi mSC samples; 50b single for 2 dpi samples) were aligned to the Zebrafish reference genome using BISMARK version 0.7.3.  (parameters -n 1 -l 28)
The BISMARK script METHYLATION_EXTRACTOR was used to extract methylation calls for every Cytosine.
CpG context files were processed using the methylKit R package version 0.5.4
Genome_build: Zv9
Supplementary_files_format_and_content: Methylation call files were generated using the methylKit R package's read() function.
Supplementary_files_format_and_content: CpG methylation calls
Supplementary_files_format_and_content: CHG methylatiion calls
Supplementary_files_format_and_content: CHH methylation calls

organism: Danio rerio

source_name: Muller glia

growth_protocol: Zebrafish were kept at 26-28 C on a 14/10 hr light/dark cycle.

extract_protocol:
Zebrafish retinas were collected in Leibovitz’s L15 medium, treated for 15 min with 1 mg/mL hyaluronidase at room temperature, and then dissociated in 0.01% (vol/vol) trypsin with frequent trituration. A single-cell suspension was confirmed by microscopy and target cell (GFP+ or GFP, lissamine morhpolino+) populations were isolated by FACS. gDNA was isolated from FACS purified cells using the Purelink Genomic DNA Mini Kit (Invitrogen) according to the manufacturer’s recommendations. The time between the harvest and DNA isolation of any sample did not exceed 3 hrs. The quantity of dsDNA from each sample was measured using a Qubit 2.0 Fluorometer.
gDNA samples were digested for 4 hrs with MspI, purified, and end-repaired and A-tailed with Klenow fragment 3’->5’ exo- (NEB). The samples were then purified and resuspended in Truseq DNA Sample Preparation (Illumina) Resuspension Buffer and submitted to a second round of adenylation followed immediately by ligation to barcoded Illumina adapters using the reagents and instructions of the Illumina TruSeq DNA Sample Preparation kit. The samples were then size selected on a 3% Nusieve 3:1 TBE gel and run at 5V/cm. Fragment sizes ranging from 160-340 bp (corresponding to 40-220 bp without adapter sequence) were excised from the gel and purified. Samples were then bisulfite converted using the EZ DNA Methylation-Direct Kit (Zymo), followed by amplification using PfuTurbo Cx Hotstart DNA Polymerase (Agilent) using the primers provided in the Illumina TruSeq DNA Sample Preparation kit. The libraries were then submitted to a second step of size selection on a 3% Nusieve 3:1 TBE gel, quality checked on an Agilent 2100 Bioanalyzer, DNA 1000 Tapestation and dsDNA quantified with a Qubit 2.0 Fluorometer. 50 ng of the final libraries were submitted for sequencing at the University of Michigan DNA Sequencing Core on an Illumina HiSeq 2000.

value: Injured, apobec2a,2b knockdown

value: 2 days post injury

value: retina


title: H1 Control BrdU-Seq Input

value: Non-Targeting siRNA


title: 2 dpi MGPC, apobec2a,2b Mo_Sample 12848


title: H1 EP300_CREBBP knockdown BrdU-Seq

value: BrdU (BD Biosciences, 347580)


title: 2 dpi MGPC, Control Mo_Sample 12846

description:
Bisulfite treated, MspI digestion
Control morpholino was delivered at the time of injury (6 x 0.7 μl of 0.25mM morpholino injections per eye) by using a Hamilton syringe. Morpholino delivery to cells was facilitated by electroporation. 6 additional lesions per eye were performed following electroporation.

value: Injured, control knockdown


title: 2 dpi MGPC, Control Mo_Sample 12845


title: H1 Control BrdU-Seq


title: FRT_input

value: Human Embryonal Kidney Cells

value: dexamethasone

value: 1 h


title: IMR90 BrdU-Seq Input


title: 4 dpi MGPC_Sample 11272

description:
Bisulfite treated, MspI digestion
12 lesions per eye were performed with a 30 guage needle

value: 1016 tub1a:gfp

value: Injured

value: 4 days post injury


title: 4 dpi MGPC_Sample 11273


title: MG_Sample 11271

description: Bisulfite treated, MspI digestion

value: Uninjured

value: 0 hours post injury


title: 3KR_dex_GR_rep2

value: GR (Santa Cruz, sc-1003, lot # D1812)

value: SUMOylation-defective GR


title: MG_Sample 11270

description: Bisulfite treated, MspI digestion


title: Dyak_ovary_rep3

status: Public on Nov 04 2013

city: Sao Paulo

first: Maria

last: Vibranovski

address: Rua do Matao, 277

department: Genetics and Evolutionary Biology

country: Brazil

institute: Universidade de Sao Paolo

data_processing:
genome_build: Drosophila yakuba release 1.3 (http://flybase.org)
Raw data processing: Illumina's Real Time Analysis v 1.13 software was used to process sequencer images, call bases, and provide base quality scores
Mapping reads to reference genomes: Bowtie v2.1.0 using default parameters and the appropriate reference genome.
Differential expression analysis: Cufflinks v 2.1.0 Cuffdiff module, default parameters.
Differential expression analysis: edgeR. Count values for genes were generated using HTseq v0.5.4p3 with options "-s no -m intersection-nonempty -a 1". Count values were full-quantile normalized within samples by gene-level GC content calculated from reference genome/annotation files and full-quantile normalized between samples before DE analysis.
Supplementary_files_format_and_content: Cuffdiff files are native Cuffdiff v2.1.0 gene_exp.diff output files. In each case, sample_1 is testis and sample_2 is ovary. Value_1 and value_2 are then the normalized expression values (FPKM) of the locus that were used in the DE analysis. Please see the software manual for additional information on the file format.
Supplementary_files_format_and_content: edgeR files are native output from edgeR's "topTags" subroutine. Information for all genes that were tested is included in this file, which consists of columns for gene ID, log2(normalized ovary expression level / normalized testis expression level), logCPM, likelihood ratios, P-values, and q-values. See the software manual for further information.

molecule: polyA RNA

organism: Drosophila yakuba

source_name: ovary

growth_protocol: All flies were grown on cornmeal-molasses agar at 25C on 12 hour light/dark cycle at ~50% humidity.

extract_protocol:
Virgin adult males and females were collected and aged 6-10 days before dissecting out testes or ovaries. All attached ducts were removed from the gonad tissue. Tissues were stored in RNAlater (Ambion) at -20C until RNA extraction. Immediately before RNA extraction RNAlater was removed by adding 1 mL RNase-free phosphate-buffered saline (PBS), centrifuging the sample 5,000 x g at 4 degrees C for 5 minutes, replacing the supernatant with 1 mL fresh PBS, centrifuging again, and replacing the supernatant with extraction buffer (XB) from the Arturus(R) PicoPure (R) kit according to the manufacturer's instructions. We included an on-column DNase digestion in the RNA extraction protocol.
Libraries were constructed following the Illumina TruSeq RNA Library Construction Kit. Poly-A+ RNA was selected, reverse-transcribed using random (hexamer) priming, and the resulting cDNA fragments sheared to ~120-200 bp fragments. These fragments were used for adapter ligation and sequencing.

value: CSN

tag: genotype

value: wild type

value: 6-10 day old adult

value: ovary


title: MHC403

city: Boston

first: Jonathan

last: Seidman

state: MA

address: 77 Avenue Louis Pasteur, NRB256

institute: Harvard Medical School

description: HCM sample

data_processing:
Basecalling with Illumina GAPipeline-1.4.0
Alignment with Tophat v1.0.14
Gene expression profiling with 5'RNA-seq software package
5pr comparisons with 5'RNA-seq software package
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary-table-1-date11021.txt: A genome-wide comparison between MHC403/+ and WT samples for changes in read distributions at 5’ ends and expression level changes. Columns: (A) Gene, (B) Description, (C) Chromosome, (D) Genome start coordinate, (E) Genome end coordinate, (F) Strand, (G) Annotated transcription start coordinates, (H) 5’ region utilized by the start-site analysis algorithm. Note that this range can be parametrically modified. Also, no upstream region is used if coordinates of another gene overlap or nearby. (I) 5’RNA-seq score, (J) Read counts normalized to 1 million total sample reads for the indicated sample, (K) Normalized read counts for the indicated sample as in J, (L) Gene read counts for the indicated sample, (M) Gene read counts for the indicated sample, (N) Fold between the two normalized read counts of the two samples as indicated, (O) Bayesian p-value comparison between the two read values.

source_name: heart

extract_protocol:
Trizol
Enhanced sequencing at 5' ends of transcripts to sensitively query chages in start-site usage (intact polyA RNA, no fragmentation of RNA or cDNA, size selection, linear amplification)

treatment_protocol: subcutaneous injection of CsA (15 mg/kg body weight in PBS, twice daily) for 2 weeks

value: 8-16 weeks


title: MDP 4

value: Adult

tag: immunogen treatment

value: MDP

tag: time after exposure

value: 1 hour


title: H1 H3K18ac ChIP-Seq

value: Embryonic stem cells

value: mTESR1 (STEMCELL Technologies)

value: Between 35 to 45

value: Custom 814 H3K18ac


title: Dyak_testis_rep1

source_name: testis

value: testis


title: Dyak_ovary_rep1


title: Dyak_ovary_rep2


title: IMR90 BrdU-Seq

value: Primary lung fibroblasts

value: DMEM supplemented with 10% FBS and 1X antibiotics

value: Between 7 to 12

value: BrdU (BD Biosciences, 347580)


title: WT

description: wild-type sample

value: wild-type


title: Dpse_ovary_rep3

data_processing:
genome_build: Drosophila pseudoobscura release 3.1 (http://flybase.org)
Raw data processing: Illumina's Real Time Analysis v 1.13 software was used to process sequencer images, call bases, and provide base quality scores
Mapping reads to reference genomes: Bowtie v2.1.0 using default parameters and the appropriate reference genome.
Differential expression analysis: Cufflinks v 2.1.0 Cuffdiff module, default parameters.
Differential expression analysis: edgeR. Count values for genes were generated using HTseq v0.5.4p3 with options "-s no -m intersection-nonempty -a 1". Count values were full-quantile normalized within samples by gene-level GC content calculated from reference genome/annotation files and full-quantile normalized between samples before DE analysis.
Supplementary_files_format_and_content: Cuffdiff files are native Cuffdiff v2.1.0 gene_exp.diff output files. In each case, sample_1 is testis and sample_2 is ovary. Value_1 and value_2 are then the normalized expression values (FPKM) of the locus that were used in the DE analysis. Please see the software manual for additional information on the file format.
Supplementary_files_format_and_content: edgeR files are native output from edgeR's "topTags" subroutine. Information for all genes that were tested is included in this file, which consists of columns for gene ID, log2(normalized ovary expression level / normalized testis expression level), logCPM, likelihood ratios, P-values, and q-values. See the software manual for further information.

organism: Drosophila pseudoobscura

growth_protocol: All flies were grown on cornmeal-molasses agar at 20C on 12 hour light/dark cycle at ~50% humidity.

value: Drosophila Species Stock Center 14011-0121.94

value: wild type


title: Dpse_ovary_rep2

value: 6-10 day old adult

value: ovary


title: DZ046_input_BriL3

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: CGCCCACT

data_processing:
All C. elegans reads were subsequently trimmed to the first 27 bases and aligned to the ce10 reference genome using Bowtie, accepting only uniquely mapped reads with up to two mismatches. For C. briggsae, 48-base reads were aligned using the same Bowtie program settings to the cb4 reference genome.
Aligned reads were extended to 200 bases, and the number of reads overlapping with each base of the genome was counted using Bedtools (Quinlan & Hall, Bioinformatics, 2010).
The per-base read counts were then normalized to the genome-wide average in order to take the sequencing depth into account.
Genome_build: ce10
Genome_build: cb4
Supplementary_files_format_and_content: Processed data files are in bigwig format representing overlappaing read counts at each base in the genome.

organism: Caenorhabditis briggsae

source_name: AF16 strain, L3 stage

growth_protocol: Gravid hermaphrodites were bleached and their eggs were  collected and allowed to hatch overnight in M9. Synchronized animals were then grown in  standard liquid culture conditions (wormbook.org) using HB101 bacteria as a food source, and  staged by gonad migration and time. N2, AF16, and tra-1(e1834)/hT2[bli-4(e937) let-?(q782)  qIs48] animals were grown at 20°C; spe-11(hc77) and glp-4(bn2) animals were grown at 25°C.  tra-1(e1834) homozygotes were sorted from tra-1(e1834)/hT2[bli-4(e937) let-?(q782) qIs48]  siblings using a COPAS BIOSORT SELECT (Union Biometrica, 350-5000-000) to collect GFPnegative  animals. Two consecutive rounds of sorting were used to ensure a pure population of  tra-1(e1834) homozygotes. Collected animals were separated from residual bacteria by sucrose  flotation and washes in M9, and then frozen in liquid nitrogen.

extract_protocol:
Insoluble material was pelleted at 12000g at 4C for 10 min. 1mL of supernatant was added to 9mL of dilution buffer. 300uL of this was set aside as an “input” sample. 2ug of TRA-1 antibody UMN163 was added to the remaining sample and incubated in a 15mL conical with rotation at 4C o/n. Samples were spun at 15000g at 4C for 15 min and supernatant was decanted into a fresh 15mL conical tube. 50ul of blocked 50% PAS beads were added and incubated with rotation at 4C for 1 hr. PAS beads were pelleted at 1000g for 30 sec and supernatant was removed. Beads were then washed once in each of the following buffers; low salt buffer, high salt buffer, LiCl buffer, Morohashi RIPA, DOC lysis buffer, and TE. Beads were then transferred to a fresh tube and washed again with TE. Each wash consisted of adding 1mL of 4C buffer, inverting for 30 seconds, spinning at 1000g at 4C for 30 sec, and then discarding the supernatant. After the final wash, residual TE was removed with a small bore pipette tip. 130uL of elution buffer was added to each sample and incubated with rotation at RT for 15 min. Beads were spun down at 1000g for 30 sec and 100uL of supernatant was transferred into a new 1.5mL tube. An additional 100uL of elution buffer was added to each sample and incubated with rotation at RT for an additional 15 min. Again, beads were spun down at 1000g for 30 sec and another 100uL of supernatant was transferred into the same 1.5mL tube, making 200uL total volume per sample. At this point, 200uL of the “input” sample was processed in parallel to the IP samples for the rest of the protocol. 10uL of 4M NaCl was added to each sample and incubated o/n at 65C. Samples were then cooled to RT, and 1uL of 10 mg/mL RNAse A was added to each sample and incubated at 37C for 30 min. Then 4uL of .5M EDTA, 8uL Tris (pH=6.5), and 1uL of PCR grade proteinase K were added to each sample and incubated at 50C for 1 hr. Samples were then purified using Qiagen PCR purification columns and eluted in 50-100uL of Qiagen EB.
DNA were blunt-ended, A-overhanged, and then ligated with adaptors. DNA libraries were amplified by PCR with single-end primers. Amplicons in the size range between 200 and 500 bp were recovered from agarose gel.

treatment_protocol: Frozen animals were physically disrupted by grinding in liquid nitrogen in a mortar and pestle,  fixed in 1%PFA in PBS for 15 min at RT and post-fixed with 50mM glycine for 5 min at RT. All  subsequent steps were performed at 4°C. Material was pelleted, washed 3x in PBS with  protease inhibitors, and resuspended in 1%SDS lysis buffer. Fixed chromatin was sheared with  a Diagenode Bioruptor Standard, on the high setting for 7.5 min total on time (15 min of 30 sec  on, 30 sec off cycles).

tag: treatment

value: no treatment

tag: chip antibody


title: DZ041_TRA1_BriL3

description: GATCTTGT

value: anti-TRA-1 antibody UMN163


title: Dpse_ovary_rep1


title: TDRD12 IP #rep1

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description: Tdrd12 +/+

data_processing:
Illumina CASAVA version 1.7 used for basecalling (?)
The adapter sequences of smallRNA reads were clipped. Both smallRNA and mRNA sequencing reads were then mapped to the respective genomes.
Genome_build: mm9 for mouse, bombyx mori genome from KAIKOGAAS
Supplementary_files_format_and_content: Tab-delimted text file includes reads and their frequencies.

source_name: Mouse testis, E18

extract_protocol: Detailed protocol can be found in Pandey et al. 2013

tag: genetic background

value: C57BL/6;129S4/SvJae mixed


title: TDRD12 IP #rep2

description: Tdrd12 +/+

tag: tissue


title: Total small RNA (14-40 nt) rep1

source_name: Mouse testis, P0


title: MSM24

city: Beijing

first: Jinhai

last: YU

address: Datun Road, NO. 15

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Sequences were mapped to whole genome, using bowtie v0.12.8 with parameters -t -S -C -p 12 -n 3 -e 500 --best --strata --shmem --chunkmbs 128 -m 6 --un
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.0.2 with parameters -I 1 -F 0.05 -j 0.05 -p 12 -G
Transcripts of the 3 conditions were merged by using cuffmerge
Gene differential expression was calculated by using cuffdiff
Genome_build: PD630
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Rhodococcus opacus

growth_protocol: 30 °C, 180 rpm incubation

extract_protocol:
Bacteria was peleted by centrifugation, RNA was extracted using Trizol reagent. rRNA was removed using Ribominus RiboMinus™ Eukaryote Kit for RNA-Seq (A10837-08), 100 ng rRNA-depleted total RNA was used to construct library.
RNA libraries were prepared for sequencing using standard Solid protocols

treatment_protocol: After incubating in LB for 48 hours, pellet bacteria and innoculated into MSM culture

value: MSM

tag: culture time

value: 24 hours


title: MSM3

value: 3 hours

tag: strain


title: DZ040_TRA1_BriL3

description: CGAGAAGT


title: LB

value: LB

value: 48 hours


title: MILI IP #rep2b

value: MILI

tag: age

value: testis


title: MIWI2 IP

description: Tdrd12 +/+


title: MILI IP #rep2a


title: MILI IP #rep1b


title: MILI IP

description: Tdrd12 +/+


title: mus musculus_NSC_RNAPII_ChiaPet_rep1

city: Singapore

first: Guoliang

last: Li

address: 60 Biopolis Street, #02-01, Genome

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description: Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET), biological replicate 1

data_processing:
Library strategy: ChIA-PET
base-calling: Software Name="Illumina RTA" Version="1.6.32.0"
alignment: BATMIS - Basic Alignment Tool for Mismatches http://code.google.com/p/batmis/
Interaction cluster calling: ChIA-PET data was processed with ChIA-PET Tool software: Li, G., Fullwood, M.J., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.S., Tennakoon, C., Wei, C.L., Ruan, Y. and Sung, W.K. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol, 11 (2). R22
Genome_build: mm9
processed data files format and content: map.gz: alignment
processed data files format and content: mm9.map.unique.txt.gz: unique alignments for both reads in paired-end reads
processed data files format and content: cluster.pet2+.xls: chromatin interaction

source_name: mouse adult brain

growth_protocol: Three cell lines, namely mouse embryonic stem cell E14, Neural stem cell NS5 and neuroshpere cells were grown under standard culture conditions and harvested at log phase.

extract_protocol: ChIA-PET: ChIPed Chromatin DNA was added in linkers with MmeI site contained at both ends and cyclized. MmeI was used to release pair end di-tags to discover the enhancer-promoter interactions. With the adding on the sequencing adaptors and 15 PCR cycles amplification, the ChIA-PET libraries were sequenced by 2x36 bp with Illumina GAIIx.

treatment_protocol: no treatment

value: neural stem cell

value: RNA Pol II (8WG16 clone, MMS-126R, Covance)


title: mus musculus_NPC_RNAPII_ChiaPet

description: Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET)

value: neurosphere cells


title: mus musculus_NSC_RNAPII_ChiaPet_rep2

description: Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET), biological replicate 2


title: mus musculus_ESC_RNAPII_ChiaPet_rep2

description: Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET), technical replicate 2

source_name: inner cell mass of blastocysts

value: embryonic stem cell


title: Total small RNA (14-40 nt) rep2


title: Dana_ovary_rep2

data_processing:
genome_build: Drosophila ananassae release 1.3 (http://flybase.org)
Raw data processing: Illumina's Real Time Analysis v 1.13 software was used to process sequencer images, call bases, and provide base quality scores
Mapping reads to reference genomes: Bowtie v2.1.0 using default parameters and the appropriate reference genome.
Differential expression analysis: Cufflinks v 2.1.0 Cuffdiff module, default parameters.
Differential expression analysis: edgeR. Count values for genes were generated using HTseq v0.5.4p3 with options "-s no -m intersection-nonempty -a 1". Count values were full-quantile normalized within samples by gene-level GC content calculated from reference genome/annotation files and full-quantile normalized between samples before DE analysis.
Supplementary_files_format_and_content: Cuffdiff files are native Cuffdiff v2.1.0 gene_exp.diff output files. In each case, sample_1 is testis and sample_2 is ovary. Value_1 and value_2 are then the normalized expression values (FPKM) of the locus that were used in the DE analysis. Please see the software manual for additional information on the file format.
Supplementary_files_format_and_content: edgeR files are native output from edgeR's "topTags" subroutine. Information for all genes that were tested is included in this file, which consists of columns for gene ID, log2(normalized ovary expression level / normalized testis expression level), logCPM, likelihood ratios, P-values, and q-values. See the software manual for further information.

organism: Drosophila ananassae

value: Drosophila Species Stock Center 14024-0371.13

value: wild type

tag: developmental stage


title: mus musculus_ESC_RNAPII_ChiaPet_rep1

description: Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET), technical replicate 1

tag: cell type


title: Dpse_testis_rep1

value: Drosophila Species Stock Center 14011-0121.94

value: 6-10 day old adult


title: Dpse_testis_rep2


title: DZ054_input_tra1homo

description: ATAGACAT

source_name: tra-1(e1834) homozygote L3 stage

value: no treatment


title: DZ052_TRA1_tra1homo

description: TCAGGACT

value: anti-TRA-1 antibody UMN163


title: Dana_testis_rep1


title: MILI IP #rep1a

value: C57BL/6;129S4/SvJae mixed


title: DZ056_input_tra1het

description: GGCTTCAT

source_name: tra-1(e1834) heterozygote L3 stage


title: DZ050_TRA1_spe11YA

description: GTTAATCT

source_name: spe-11(hc77) yound adult


title: DZ043_TRA1_glp4YA

description: TCAGGACT

source_name: glp-4 (bn2) yound adult


title: DZ042_TRA1_glp4YA

description: GTTAATCT


title: DZ048_input_glp4YA

description: GGCTTCAT


title: Dana_testis_rep2


title: DZ055_TRA1_tra1het

description: CGCCCACT


title: DZ039_TRA1_N2L2

description: CACGTCGT

source_name: N2 strain, L2 stage


title: dRF16: d10 ES Xist CHART

city: Farmington

first: Stefan

middle: F

last: Pinter

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health

data_processing:
Library strategy: CHART-Seq
Basecalls performed using Illumina software, version 1.8, except for dSP20b, which was performed using version 1.3
CHART-seq: Alignment was performed with Novoalign 3.00 (www.novocraft.com) using default parameters with modifications: -t 180 -h 180 180 -v 180. Uniquely aligned pairs were selected, discarding duplicate fragments. SPP was used to normalize each sample to its corresponding input accepting all tags and smoothing with 1000 kb windows sampled every 500bp. To normalize across data sets, each bedGraph was normalized to sum of all positive values on chr4.
RNA-seq: Adapter sequences were stripped from reads and identical reads discarded. Alignment was performed using tophat2 with the “b2-sensitive” preset and otherwise default parameters. After removal of PCR duplicates, all unique reads mapping to gene bodies were summed up for the cas, mus and comp tracks. Read numbers over genes in the allelic tracks were used to calculate skew (mus-cas/mus+cas) and genes skewed significantly (P < 0.01, cumulative binomial probability) in d7 ES cells and MEFs output to bedGraph.
Each dataset was aligned to variant CAST/EiJ and 129S1/SvJm genomes constructed using high quality polymorphisms to the C57/Bl6 reference genome (mm9 build). Pairs aligning to only one variant genome and pairs aligning better to one variant genome (in number of nucleotide edits to reference) than the other were retained (allele-specific), as were pairs aligning equally well (non-allele-specific).
Repetitive alignments, duplicate reads and low quality reads were removed. The resulting files were analyzed using SPP software. In this analysis all tags were included and the coverage generated with smoothing using 1kb bins every 500 bp to generate input-subtracted, normalized read densities. To account for different read depths across data sets, each coverage file was scaled using the total positive read density on an autosome (chr4) from the corresponding composite track (i.e., the mus, cas and comp tracks were all scaled using the same factor) and output to bedGraph.
CHIP-seq: Data from GSE36905 was aligned and processed as CHART-seq samples. Resulting coverage tracks (EZH2/K27me3) are included in the processed data files (bedGraphs).
Genome_build: mm9
Supplementary_files_format_and_content: All processed data files are in bedGraph format and represent either spp enrichment score for CHART-seq and CHIP-seq or skewed expression value ranging from -1 (all CAST/EiJ) to +1 (all 129S1) for RNA-seq

source_name: d10 ES Xist CHART

growth_protocol: Cells were cultured in regular fibroblast medium (1% Pen/Strep, 1% L-glutamine, high-glucose DMEM) with either 15% FBS (MEFs) or 30% FBS (ES cells)

extract_protocol:
Nuclei, purified from cells crosslinked in 1% formaldehyde for 10 min, were further crosslinked with 3% formaldehyde for 30 min at room temperature.  Sheared chromatin, with a median size around 3kb, was incubated overnight with a mixture of biotinylated capture oligonucleotides that were complementary to Xist RNA.  The hybridized material was captured by streptavidin beads, and washed extensively before RNaseH elution. Enriched DNA was purified after formaldehyde crosslink reversal and subjected to library construction.
Genome DNA of inputs and Xist CHART enriched DNA samples were fragmented by sonication, and the sequencing libraries was constructed by first repairing DNA-ends, A-tailing, ligating to universal adapters, and amplifying for 12 cycles with indexed primer.

treatment_protocol: d0 ES cells were cultured in the presence of LIF under adherent conditions. d7 ES cells were cultured without LIF under non-adherent conditions for 4 days and plated for an additional 3 days.

value: F2:129S1/CastEiJ x 129S1

value: differentiating mouse ES cells (day 10)

tag: capture oligos

tag: sequenced molecule

value: Xist CHART enriched DNA


title: DZ044_input_N2L2

description: ATAGACAT


title: DZ038_TRA1_N2L2

description: AGATGGTT


title: dRF2: d7 ES rep Xist CHART

data_processing:
Library strategy: CHART-Seq
Basecalls performed using Illumina software, version 1.8, except for dSP20b, which was performed using version 1.3
CHART-seq: Alignment was performed with Novoalign 3.00 (www.novocraft.com) using default parameters with modifications: -t 180 -h 180 180 -v 180. Uniquely aligned pairs were selected, discarding duplicate fragments. SPP was used to normalize each sample to its corresponding input accepting all tags and smoothing with 1000 kb windows sampled every 500bp. To normalize across data sets, each bedGraph was normalized to sum of all positive values on chr4.
RNA-seq: Adapter sequences were stripped from reads and identical reads discarded. Alignment was performed using tophat2 with the “b2-sensitive” preset and otherwise default parameters. After removal of PCR duplicates, all unique reads mapping to gene bodies were summed up for the cas, mus and comp tracks. Read numbers over genes in the allelic tracks were used to calculate skew (mus-cas/mus+cas) and genes skewed significantly (P < 0.01, cumulative binomial probability) in d7 ES cells and MEFs output to bedGraph.
Each dataset was aligned to variant CAST/EiJ and 129S1/SvJm genomes constructed using high quality polymorphisms to the C57/Bl6 reference genome (mm9 build). Pairs aligning to only one variant genome and pairs aligning better to one variant genome (in number of nucleotide edits to reference) than the other were retained (allele-specific), as were pairs aligning equally well (non-allele-specific).
Repetitive alignments, duplicate reads and low quality reads were removed. The resulting files were analyzed using SPP software. In this analysis all tags were included and the coverage generated with smoothing using 1kb bins every 500 bp to generate input-subtracted, normalized read densities. To account for different read depths across data sets, each coverage file was scaled using the total positive read density on an autosome (chr4) from the corresponding composite track (i.e., the mus, cas and comp tracks were all scaled using the same factor) and output to bedGraph.
CHIP-seq: Data from GSE36905 was aligned and processed as CHART-seq samples. Resulting coverage tracks (EZH2/K27me3) are linked directly to GSE48649 (bedGraphs).
Genome_build: mm9
Supplementary_files_format_and_content: All processed data files are in bedGraph format and represent either spp enrichment score for CHART-seq and CHIP-seq or skewed expression value ranging from -1 (all CAST/EiJ) to +1 (all 129S1) for RNA-seq

source_name: d7 ES rep Xist CHART

value: differentiating mouse ES cells (day 7)


title: dRF7: d7 ES input

source_name: d7 ES input

value: genomic DNA of input


title: Dana_ovary_rep1

value: ovary


title: dRF28: d3 ES rep Xist CHART

source_name: d3 ES rep Xist CHART

value: differentiating mouse ES cells (day 3)


title: dRF9: d3 ES Xist CHART

source_name: d3 ES Xist CHART


title: dRF23: 8h.LNA-4978 rep Xist CHART

description: 8 hr post tranfection of LNA-4978

source_name: 8h.LNA-4978 rep Xist CHART

value: F1:129S1/CastEiJ x 129S1

value: immortalized MEFs


title: dRF27: d0 ES rep Xist CHART

source_name: d0 ES rep Xist CHART

value: undifferentiated mouse ES


title: dRF12: 8h.LNA-4978 Xist CHART

description: 8 hr post tranfection of LNA-4978

source_name: 8h.LNA-4978 Xist CHART


title: dRF22: 3h.LNA-4978 rep Xist CHART

description: 3 hr post tranfection of LNA-4978

source_name: 3h.LNA-4978 rep Xist CHART


title: dRF10: 1h.LNA-4978 Xist CHART

description: 1 hr post tranfection of LNA-4978

source_name: 1h.LNA-4978 Xist CHART


title: dRF26: 24h.LNA-C1 Xist CHART

description: 24 hr post tranfection of LNA-C1

source_name: 24h.LNA-C1 Xist CHART


title: dRF24: 3h.LNA-C1 rep Xist CHART

description: 3 hr post tranfection of LNA-C1

source_name: 3h.LNA-C1 rep Xist CHART


title: dRF29: d10 ES rep Xist CHART

source_name: d10 ES rep Xist CHART


title: dRF25: 8h.LNA-C1 Xist CHART

description: 8 hr post tranfection of LNA-C1

source_name: 8h.LNA-C1 Xist CHART


title: dRF15: 3h.LNA-C1 Xist CHART

description: 3 hr post tranfection of LNA-C1

source_name: 3h.LNA-C1 Xist CHART


title: dRF11: 3h.LNA-4978 Xist CHART

description: 3 hr post tranfection of LNA-4978

source_name: 3h.LNA-4978 Xist CHART


title: dRF14: 1h.LNA-C1 Xist CHART

description: 1 hr post tranfection of LNA-C1

source_name: 1h.LNA-C1 Xist CHART


title: dRF18: MEF Xist CHART sense oligo

source_name: MEF Xist CHART sense oligo

value: sense control caputure oligo to C11


title: dRF6: MEF input

source_name: MEF input


title: dSP22c: rRNA-depleted total RNA

data_processing:
Basecalls performed using Illumina software, version 1.8, except for dSP20b, which was performed using version 1.3
CHART-seq: Alignment was performed with Novoalign 3.00 (www.novocraft.com) using default parameters with modifications: -t 180 -h 180 180 -v 180. Uniquely aligned pairs were selected, discarding duplicate fragments. SPP was used to normalize each sample to its corresponding input accepting all tags and smoothing with 1000 kb windows sampled every 500bp. To normalize across data sets, each bedGraph was normalized to sum of all positive values on chr4.
RNA-seq: Adapter sequences were stripped from reads and identical reads discarded. Alignment was performed using tophat2 with the “b2-sensitive” preset and otherwise default parameters. After removal of PCR duplicates, all unique reads mapping to gene bodies were summed up for the cas, mus and comp tracks. Read numbers over genes in the allelic tracks were used to calculate skew (mus-cas/mus+cas) and genes skewed significantly (P < 0.01, cumulative binomial probability) in d7 ES cells and MEFs output to bedGraph.
Each dataset was aligned to variant CAST/EiJ and 129S1/SvJm genomes constructed using high quality polymorphisms to the C57/Bl6 reference genome (mm9 build). Pairs aligning to only one variant genome and pairs aligning better to one variant genome (in number of nucleotide edits to reference) than the other were retained (allele-specific), as were pairs aligning equally well (non-allele-specific).
Repetitive alignments, duplicate reads and low quality reads were removed. The resulting files were analyzed using SPP software. In this analysis all tags were included and the coverage generated with smoothing using 1kb bins every 500 bp to generate input-subtracted, normalized read densities. To account for different read depths across data sets, each coverage file was scaled using the total positive read density on an autosome (chr4) from the corresponding composite track (i.e., the mus, cas and comp tracks were all scaled using the same factor) and output to bedGraph.
CHIP-seq: Data from GSE36905 was aligned and processed as CHART-seq samples. Resulting coverage tracks (EZH2/K27me3) are linked directly to GSE48649 (bedGraphs).
Genome_build: mm9
Supplementary_files_format_and_content: All processed data files are in bedGraph format and represent either spp enrichment score for CHART-seq and CHIP-seq or skewed expression value ranging from -1 (all CAST/EiJ) to +1 (all 129S1) for RNA-seq

source_name: rRNA-depleted total RNA

extract_protocol:
RNA greater than 200 nt from d7 ES cells and MEFs was harvested using the mirVana RNA extraction kit (Ambion), cleared of ribosomal RNA (Ribozero, Epicentre) and sheared to a median size of 200 nt, followed by library construction.
RNA fragments were end-repaired (T4 polynucleotide kinase, NEB), ligated to 3' linker (T4 RNA ligase2 trunc., NEB), reverse transcribed (Superscript III, Invitrogen) and ligated to a 3’linker on the previous 5' end. This single-stranded cDNA library was then amplified (Phusion, NEB) using custom oligos matching the Illumina TruSeq PCR primers.

tag: passage

value: passage 27

value: rRNA-depleted (Ribozero) total RNA


title: dRF13: MEF Xist CHART 40 C-oligo

source_name: MEF Xist CHART 40 C-oligo


title: dRF8: d7 ES Xist CHART

source_name: d7 ES Xist CHART


title: DZ023_TRA1_spe11YA

source_name: spe-11(hc77) yound adult


title: dRF4: MEF Xist CHART

source_name: MEF Xist CHART


title: H9 ES-derived neural precursor cells MBD-Seq

city: Daejeon

first: Mirang

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: KRIBB(Korea Research Institute of Bioscience and Biotechnology

data_processing:
The sequences were mapped to the human genome (UCSC hg18) using the Illumina Genome Analyzer data analysis pipeline.
The entire genome was divided into 200-bp segments, and the number of reads was counted in each segment. The number of reads was normalized in MES (methylation enrichement score). MES is a normalized abundance measurement for 5hmC or 5mC reads aligned on each 200-bp bin of the genome and was calculated from the number of mapped 5hmC or 5mC reads on each bin divided by the bin size (200bp) and the total number of mapped sequence reads on the genome and multiplied by the human genome size.
Genome_build: hg18
Supplementary_files_format_and_content: BED files were generated based-on the normalized read depth mapped on each 200-bp bin of the genome.

source_name: Neural precursor cells

growth_protocol: Differentiation of the hES cell line H9 (WiCell, Madison, WI, USA; passages 35-38) into NP cells and terminally into DA neurons was performed as described (Ko et al., 2007).

extract_protocol:
MBD-Seq: Genomic DNA was fragmented to 100–500 bp using nebulizer (Illumina) and then subjected to methylated DNA enrichment using the MethylMiner methylated DNA enrichment kit (Invitrogen). Briefly, methylated DNA was precipitated from 1 µg fragmented genomic DNA via binding to the methyl-CpG binding domain of human MBD2 protein, which was coupled to magnetic Dynabeads. The purified methylated DNA fragments were ligated to a pair of adaptors for sequencing on the Illumina Genome Analyzer. The ligation products were size fractioned to obtain 200–300 bp fragments on a 2% agarose gel and subjected to 18 cycles of PCR amplification.
hMeDIP-Seq: Genomic DNA was fragmented to 150–250 bp by 60 psi of nitrogen gas for 7 minute through a nebulizer (Illumina) and then subjected to library preparation using genomic DNA sample prep kit (Illumina). Briefly, 5 µg fragmented DNA was end-repaired, A-tailed and ligated to paired-end adapters. The pre-adapted DNA was subjected to immunoprecipitation using hMeDIP kit (Diagenode, Catalog No. AF-110-0016). Briefly, 1 µg of the pre-adapted DNA was denatured for 10 minutes at 95 oC and incubated with the 2.5 µg of mouse monoclonal anti-5hmC antibody (Diagenode) for 2 hours at 4 oC. The immunoabsorbed DNA was recovered after incubating with anti-mouse IgG-coated magnetic beads (Diagenode) at 4 oC for overnight. The immunoprecipitated DNA was amplified by 18 cycles of PCR using illumina PCR primers and then size fractioned to obtain 200–300 bp fragments on a 2% agarose.
Cluster generation and 72 cycles of single-read sequencing were done.

value: ES-derived neural precursor cells

tag: parental cell line

tag: quantification

value: MethylFlash methylated DNA quantification kit (Epigentek, Catalog No. P-1035)


title: dRF5: d0 ES Xist CHART

source_name: d0 ES Xist CHART


title: DZ012_TRA1_N2L3

description: no barcode

source_name: N2 strain, L3 stage

value: no treatment

value: anti-TRA-1 antibody UMN163


title: dSP22t: rRNA-depleted total RNA


title: dSP20b: rRNA-depleted total RNA

value: F2:129S1/CastEiJ x 129S1

value: differentiating mouse ES cells (d7)


title: H9 ES-derived neural precursor cells hMeDIP-Seq

tag: antibody

tag: antibody manufacturer

value: Diagenode

value: MethylFlash hydroxymethylated DNA quantification kit (Epigentek, Catalog No. P-1036)


title: H9 ES-derived dopamine neuron cells hMeDIP-Seq

source_name: Dopamine neuron cells

value: ES-derived dopamine neuron cells


title: DZ014_input_N2L3

description: no barcode


title: H9 Embryonic stem (ES) cells MBD-Seq

source_name: Embryonic stem cells

value: Embryonic stem cells H9

tag: passages

tag: cell line


title: H1546_exp

status: Public on Nov 03 2013

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description: In the processed data file the values for each chromosome were generated by dividing by the following factors, main chromosome: 0.8; pHV1: 0.3; pHV3: 0.85.

data_processing:
Sequence reads were mapped to the H. volcanii reference genome (Accession numbers: CP001953-CP001957) using BioScope (version 1.3.1).
Sequence reads mapping to a single genomic location were summed in 1 kb bins.
Normalised copy numbers were generated by dividing the sequence read counts from the exponential (replicating) sample by counts from the stationary (non-replicating) sample for each strain.
Normalised copy numbers were manually adjusted to give a minimum ratio of ~1 for each chromosome.
Genome_build: CP001953-CP001957
Supplementary_files_format_and_content: Wig file containing normalised replication profile for the main chromosome (reconstructed where appropriate), pHV1,  pHV3 and (where appropriate) pHV4. Each chromosome is individually normalised to give a minimum of ~1.

organism: Haloferax volcanii

source_name: Genome DNA from cells in exponential phase (A650 =~ 0.1)

growth_protocol: H. volcanii strains were grown as described previously [PMID: 14766575]. Genomic DNA was isolated from 100 ml culture in stationary phase (A650 >1) or ~1 L in exponential phase (A650 ~0.1).

extract_protocol:
SDS lysis, ethanol precipitation, RNaseA treatment, phenol-chloroform extraction as described previously [PMID: 14766575].
Library preparation and sequencing was carried out according to SOLiD instructions.

tag: relevant genotype

value: ∆pyrE2 ∆trpA ∆oriC1 ∆oriC2 ∆oriC3 ∆ori-pHV4::trpA+

tag: growth phase

value: exponential


title: BmTdrd12 IP

description: Endogenous BmTdrd12-IP from BmN4 cells

organism: Bombyx mori

source_name: Bombyx mori, BmN4 cells

tag: sample type

value: Endogenous BmTdrd12-IP from BmN4 cells

tag: genetic background

value: C57BL/6;129S4/SvJae mixed


title: dSP22g: rRNA-depleted total RNA

organism: Mus musculus

tag: strain


title: Osr1f/-; Wnt1cre tongue

city: cincinnati

first: HAN

last: LIU

state: oh

address: 3333 burnet avenue

department: DEVELOPMENTAL BIOLOGY

institute: CINCINNATI CHILDREN'S HOSPITAL

data_processing:
Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.Implanted in tophat 1.4.1 using parameters:tophat -G mm9.gtf -o tophat -p 4 -r 0 mm9 reads.fastq. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Osr1 mutant mouse embryonic tongue

extract_protocol:
E12 mouse embryonic tongues were micro-dissected in cold PBS, immediately frozen at -80℃, total RNA was extracted by using RNeasy micro kit from Qiagen.
cDNA was made by the NuGEN Ovation RNA-Seq v2 Assay.

value: mixed background

tag: tissue

value: embryonic tongue

tag: genotype/variation

value: Osr1f/-; Wnt1cre

tag: age

value: emrbyonic day 12


title: H1546_stat

source_name: Genome DNA from cells in stationary phase (A650 > 1)

value: stationary


title: H1374_exp

description: In the processed data file the values for each chromosome were generated by dividing by the following factors, main chromosome: 0.75; pHV1: 0.5; pHV3: 1.2.

value: ∆pyrE2 ∆trpA ∆oriC1 ∆oriC2 ∆oriC3::trpA+


title: DZ015_TRA1_N2L3

description: no barcode

tag: treatment

value: no treatment

tag: chip antibody

value: anti-TRA-1 antibody UMN163


title: H1374_stat


title: H9 ES-derived dopamine neuron cells MBD-Seq

tag: cell type

value: MethylFlash methylated DNA quantification kit (Epigentek, Catalog No. P-1035)