title: Uninfected polysomal Set 3

status: Public on Sep 21 2012

city: Blacksburg

first: Jinsong

last: Zhu

state: VA

address: 313 Engel Hall

department: Biochemistry

institute: Virginia Tech

data_processing:
Illumina Casava1.6 software used for basecalling and demultiplexing; adaptor removal using a perl script. These steps conducted by Virginia Bioinformatics Institute.
Convert Fastq to Fasta using Tu lab program "fastq_to_fasta"  (Jake Tu, Virginia Tech)
Format Fasta using the program "formatdb"
BLAST:  Blastn against An. gambiae database using the following conditions:  -p blastn -a 12 -m 8 -v 1000000 -b 1000000  -e 1e-20 -m 8 -d
Tally results:  Count number of hits for each query using Tu lab program "Count_query.pl"  and merge results into a single table with the Tu lab program "mergeHitCount_adv.pl"  (Jake Tu, Virginia Tech)
Genome_build: An. gambiae P3.4 CDNA ALL from Vectorbase
Supplementary_files_format_and_content: Excel file includes RPM (Reads Per Million) values for each sample and the calculated relative polysome loading for each mRNA species.

organism: Anopheles gambiae

source_name: midgut

extract_protocol: Two hundred female mosquitoes were dissected at 22-26 hours post blood meal to obtain midguts. The samples were flash frozen in liquid nitrogen and stored at -80ºC until processed. Frozen samples were ground using a mortar and pestle, homogenized in 1 ml lysis buffer (15 mM Tris-HCl, pH 8.0, 300 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mg/ml cycloheximide, 1 mg/ml heparin, 1% triton X-100, 0.2 U/ml RNase inhibitor). The extracts were spun 15 minutes at 14,000 rpm at 4ºC to remove cell debris and nuclei. An aliquot of the supernatant was saved for analysis of total cellular mRNA. The rest of the supernatant was directly applied to the top of a 10-60% linear sucrose gradient that was prepared as described by Arava, containing 20 mM Tris–HCl (pH 8), 140 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mg/ml cycloheximide, and 0.5 mg/ml heparin. Centrifugation was carried out using an SW41-Ti rotor at 116,000×g for 3 hours at 4ºC. Following spinning, gradient fractions were collected immediately using a Density Gradient Fractionation System (Brandel, Gaithersburg, MD) with simultaneous recording of absorbance profiles at 254 nm. Following fractionation, non-polysomal aliquots were pooled together into one sample, and polysomal aliquots were pooled into a second sample. The fraction between was discarded to ensure good separation. RNA samples from three independent infection experiments were collected. For each set, we had six RNA samples: polysomal and nonpolysomal RNAs of the infected mosquitoes, polysomal and nonpolysomal RNAs of the uninfected controls, and total cellular mRNAs of the infected and uninfected mosquitoes. A fourth set of samples were maintained as individual fractions for qRT-PCR analysis of specific transcripts. RNA was extracted from the fractionated and unfractionated samples using Trizol reagent (Invitrogen, Carlsbad, CA). Sample preparation for Illumina-based mRNA sequencing was conducted based upon the manufacturer’s protocols “mRNA Sequencing Sample Preparation Guide” and “Preparing Samples for Multiplexed Paired-End Sequencing” (Part# 1005361Rev B, and Part# 1004898Rev D, Illumina, Inc., San Diego, CA). For each set, six cDNA libraries derived from the six RNA samples were uniquely tagged with index sequences at the PCR stage of sample preparation. Six libraries were pooled together and sequenced in a single lane of a flow cell. 76-cycle single read Illumina sequencing was conducted at the Virginia Bioinformatics Institute (VBI, Blacksburg, VA).

treatment_protocol: Gametocytes were harvested and used immediately in bloodfeeding of mosquitoes. Female adult An. gambiae (G3 strain) mosquitoes were maintained on 10% sucrose at 27ºC/80% humidity. Prior to bloodfeeding, the mosquitoes (4-6 days post-eclosion) were maintained overnight on water only. Bloodfeeding was carried out using a Hemotek 5W1 system and collagen Hemotek feeding membranes (Discovery Workshops, Lancashire, England). Mosquitoes were allowed to feed for 15 minutes. This resulted in bloodfeeding of approximately 80-90% of available Anopheles gambiae females. A control group of mosquitoes were fed on uninfected blood and serum by essentially the same method.

tag: time post bloodmeal

tag: gender

value: female

tag: infection status

value: uninfected control


title: Uninfected unfractionated Set 3

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: strain


title: Infected nonpolysomal Set 3

value: infection with P. falciparum 3D7G


title: Infected unfractionated Set 2


title: Infected unfractionated Set 3


title: Uninfected unfractionated Set 2


title: Uninfected nonpolysomal Set 2


title: E14 day6 5-hmC ChIP-seq

status: Public on Sep 22 2012

city: La Jolla

first: Pengfei

last: Yu

state: CA

address: 9500 Gilman Drive MC 0419

department: Bioengineering

institute: University of California San Diego

library_source: genomic

data_processing:
The libraries for ncRNA and 5-hmC were sequenced on a HiSeq2000 using a TruSeq SBS sequencing kit version 2 and analyzed with pipeline version 1.8. The libraries of MeDIP-seq and MRE-seq were sequenced on Illumina GAII.
For small ncRNA sequencing data, The 3’ adapters were first trimmed from all 40bp short sequencing reads and short reads (<18bp) were removed after trimming. After that, reads were mapped into mouse mm9 genome using bowtie software with no mismatch in the first 18 seed sequences, and with no more than 5 alignments in the genome. Only the best alignments for each mappable reads were reported.
MRE-seq data were generated by index-sequencing(each index has 7bp), and total length of each sequenced read is 49bp. so the valid length of each read is 42bp. After trimming the indexes, the 42bp reads were mapped to mm9 genome by MAQ with an additional constraint that the 5′ end of a read must map to the CpG site within a MRE site
MeDIP-seq data were mapped to mm9 genome by MAQ
Sequence reads for 5hmC were mapped to mm9 using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome_build: mm9
Supplementary_files_format_and_content: BED

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells (E14)

growth_protocol: E14(mESC) were plated onto gelatin-coated dishes in Dulbecco's modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM -mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Millipore ESG1107) in incubator set at 37 ºC in 5% CO2.

extract_protocol: MRE-seq was performed as described (NATURE| Vol 466|8 July 2010). Four parallel digests were performed (HpaII, Hin6I and SsiI are from Fermentas; HpyCH4IV is from NEB), each with 1 ug of DNA. Five units of enzyme per microgram DNA were added and incubated at 37˚C for 3 hrs. A second dose of five units-enzyme was added and the DNA was incubated for an additional 3 hrs. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose gel. A 100-500 bp gel slice was excised and gel-purified using Qiagen Qiaquick columns, eluting in 30 ul of Qiagen EB buffer. Library construction was performed using the Illumina Genomic DNA Sample kit with paired-end adapters, following the manufacturer’s instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the klenow DNA polymerase was diluted 1:5 in water and 1 ul used per reaction. For paired-end oligo adapter ligation, adapters were diluted 1:10 in water and 1 ul used per reaction. After the second size selection, DNA was eluted in 36 ul EB buffer using Qiagen Qiaquick columns, and 12 ul used as template for PCR, using Illumina reagents and cycling conditions with 15 cycles. After cleanup with Qiagen MinElute columns, each library is examined by Quant-iT™ dsDNA HS Assay Kit (Qubit, Invitrogen, USA) and Agilent DNA Biaanalyzer (Agilent, USA). MeDIP-seq was performed as described (NATURE| Vol 466|8 July 2010). 3 ug DNA isolated as described above was sonicated to ,100–500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to paired-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 1 ug of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg/ml, Eurogentec). For this, DNA was heat-denatured at 95 ˚C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 ul primary antibody per microgram of DNA overnight at 4 ˚C with rocking agitation in 500 ml immunoprecipitation buffer (10mMsodium phosphate buffer, pH 7.0, 140mMNaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 2ul of rabbit anti-mouse IgG secondary antibody (2.5 mg/ml, Jackson Immunoresearch) and 100 ml Protein A/G beads (Pierce Biotechnology) were added and incubated for an additional 2 h at 4 ˚C with agitation. After immunoprecipitation a total of six to ten immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. A nonspecific mouse IgG immunoprecipitation (Jackson Immunoresearch) was performed in parallel to methyl DNA immunoprecipitation as a negative control. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/ml proteinase K for 2 h at 55 ˚C and then allowed to cool to room temperature. MeDIP and supernatant DNA were purified using Qiagen Qiaquic columns and eluted in 30 ul EB (Qiagen). Twelve cycles of PCR were performed on 10 ul of the immunoprecipitated DNA using the paired-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (192–592 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis. An aliquot of each library was diluted in EB to 5 ng/ul and 1 ul used as template in four independent PCR reactions to confirm enrichment for methylated and de-enrichment for unmethylated sequences, compared to 5 ng of input (sonicated DNA). Two positive controls (SNRPN and MAGEA1 promoters) and two negative controls (a CpG-less sequence on chromosome 15 and GAPDH promoter) were amplified (Supplementary). Cycling was 95 ˚C for 30 s, 58 ˚C for 30 s, 72 ˚C for 30 s with 30 cycles. PCR products were visualized by 1.5% agarose gel electrophoresis. DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. Biotechnol. 2011, 29, 68-72). For ncRNA-seq, Total RNA was purified by Trizol Reagent (Invitrogen) and used as input to generate microRNA library by True-seq small RNA kit (Illumina). The RNA 3’ adapter is specifically modified to target microRNAs and other small RNAs that have a 3’ hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. The bands of library products from 145-160bp were cut and amplified for sequencing. The libraries were then quantitated by qPCR.

treatment_protocol: Guided differentiation procedures were preformed as following: 2×105 cells were seeded on the Collagen IV coated 10cm dishes (BD, 08-774-33) in serum free medium ESF-B (Itochu Corporation) supplemented with 0.1%BSA, 50M 2-Me and 10 ng/ml Activin A. Mediums were changed every day. Genomic DNAs and total RNAs were collected in day0, 4, and 6.

tag: development stage

value: Day 6

tag: cell type

value: mouse embryonic stem cells (E14)

tag: treatment

value: activin

tag: genetic background


title: E14 day4 5-hmC ChIP-seq

value: Day 4


title: Infected unfractionated Set 1


title: Infected nonpolysomal Set 2


title: Uninfected unfractionated Set 1


title: Uninfected polysomal Set 1


title: Infected polysomal Set 1


title: Infected nonpolysomal Set 1


title: Uninfected nonpolysomal Set 1


title: Tag_seq_eye-antennal_imaginal_disc_D.virilis

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

data_processing:
The base-calling software was Bustard1.4.0 (Bentley et al. 2008).
Mapping to corresponding species genome [Drosophila melanogaster 5; Drosophila yakuba FB1 / UCSC droYak2; Drosophila virilis FB1 / UCSC droVir3] using bowtie version 0.12.1 allowing two mismatches. Only uniquely mapped reads were taken into consideration.

File: positions.txt
Mapped total counts. Mappings were performed using bowtie (Langmead et al. 2009) with maximally two mismatches per read.

Genome_build: Drosophila virilis FB1 / UCSC droVir3
Supplementary_files_format_and_content: positions.txt files contain the mapped positions assigned to a gene and the number of counts per position.

organism: Drosophila virilis

source_name: third instar wandering larvae eye-antennal imaginal disc

extract_protocol: Illumina TAG-Profiling protocol. Restriction enzyme NlaIII.

tag: developmental stage

value: third instar wandering larvae

tag: tissue

value: eye-antennal imaginal disc


title: Uninfected polysomal Set 2


title: Tag_seq_wing_imaginal_disc_D.virilis

source_name: third instar wandering larvae wing imaginal disc

value: wing imaginal disc


title: Tag_seq_eye-antennal_imaginal_disc_D.melanogaster

data_processing:
The base-calling software was Bustard1.4.0 (Bentley et al. 2008).
Mapping to corresponding species genome [Drosophila melanogaster 5; Drosophila yakuba FB1 / UCSC droYak2; Drosophila virilis FB1 / UCSC droVir3] using bowtie version 0.12.1 allowing two mismatches. Only uniquely mapped reads were taken into consideration.

File: positions.txt
Mapped total counts. Mappings were performed using bowtie (Langmead et al. 2009) with maximally two mismatches per read.

Genome_build: Drosophila melanogaster 5
Supplementary_files_format_and_content: positions.txt files contain the mapped positions assigned to a gene and the number of counts per position.

organism: Drosophila melanogaster

value: CantonS


title: Tag_seq_wing_imaginal_disc_D.yakuba

data_processing:
The base-calling software was Bustard1.4.0 (Bentley et al. 2008).
Mapping to corresponding species genome [Drosophila melanogaster 5; Drosophila yakuba FB1 / UCSC droYak2; Drosophila virilis FB1 / UCSC droVir3] using bowtie version 0.12.1 allowing two mismatches. Only uniquely mapped reads were taken into consideration.

File: positions.txt
Mapped total counts. Mappings were performed using bowtie (Langmead et al. 2009) with maximally two mismatches per read.

Genome_build: Drosophila yakuba FB1 / UCSC droYak2
Supplementary_files_format_and_content: positions.txt files contain the mapped positions assigned to a gene and the number of counts per position.

organism: Drosophila yakuba


title: Tag_seq_eye-antennal_imaginal_disc_D.yakuba


title: at-sperm-col_wt

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

description: Arabidopsis thaliana sperm of Columbia-0 (female).

data_processing:
Alignment: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted  Col and Ler scaffolds, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases. 80 base reads were divided into the first 40 and the last 40 bases. 100 base reads were divided into the first 50 and the last 50 bases. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first. Reads that aligned to either Col or Ler with fewer mismatches were assigned to that ecotype.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Genome_build: TAIR8
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

organism: Arabidopsis thaliana

source_name: AT Sperm Columbia

extract_protocol: About 150 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen) as outlined in the manufacturer’s instructions. One quarter of the bisulfite-converted libraries was PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). PCR reactions were carried out as follows: 95 ̊C 3 min, then 12-14 cycles of 95 ̊C 30 sec, 65 ̊C 30 sec and 72 ̊C 60 sec. The enriched libraries were purified twice with solid phase reversible immobilization (SPRI) method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).

treatment_protocol: Stage 12-13 flower buds were emasculated and pollinated 48 hours later. Reciprocal crosses were performed using wild-type Col-0 and Ler ecotypes. In addition, dme-2 (Col-gl) heterozygous flowers were pollinated with wild-type (Ler) pollen, and fie-1 (Ler) heterozygous flowers were pollinated with wild-type (Col-0) pollen. For wild-type crosses, seven to eight days after pollination, F1 seeds (torpedo-stage to early-bent-cotyledon stage) were immersed in 0.3 M sorbitol and 5 mM Mes (pH 5.7) on a slide under a dissecting microscope. Embryo and endosperm were dissected using a fine needle and forceps. The seed coat was discarded. Wild-type embryos were twice centrifuged and the pellet resuspended in 0.3 M sorbitol and 5 mM Mes (pH 5.7) to remove contaminating endosperm. For crosses with the dme-2 or fie-1 mutations, F1 aborting seeds were identified and mutant endosperm was isolated. Approximately 500 wild-type endosperm, 1000 dme-2 or fie-1 endosperm, and 300 wild-type embryos were collected. Pollen was isolated from wild-type (Col-0) and dme-2 heterozygous plants (Col-gl ecotype) as described previously. Vegetative cell and sperm nuclei were extracted from mature pollen and fractionated by fluorescence activated cell sorting as described previously.

tag: tissue type

value: pollen


title: Uninfected nonpolysomal Set 3


title: RNA_seq_eye-antennal_imaginal_disc_gl[60j]_rep2

data_processing:
The base-calling method is included in the CASAVA v1.8 pipeline.
RNA-Seq reads were mapped to D. melanogaster genome (dm3) using TopHat v.2.0 (default parameters) (Trapnell et al. 2009). Gene expression measures were computed by HT-Seq (Anders and Huber 2010) (option -str=no) using D.melanogaster gene annotation FlyBase release 5.30.
Genome_build: dm3
Supplementary_files_format_and_content: counts files include RNA abundance counts

source_name: third instar wandering larvae eye-antenna imaginal disc

extract_protocol: Illumina TruSeq protocol

tag: genotype/variation

value: glass mutant (gl[60j])


title: Infected polysomal Set 3


title: Tag_seq_wing_imaginal_disc_D.melanogaster


title: Infected polysomal Set 2


title: RNA_seq_eye-antennal_imaginal_disc_wild-type [CantonS]

value: wild-type


title: at-sperm-col_dme2

description: Arabidopsis thaliana sperm of dme-2 Columbia-gl (female).

source_name: AT Sperm dme-2 Columbia


title: RNA_seq_eye-antennal_imaginal_disc_gl[60j]_rep1


title: RNA_seq_eye-antennal_imaginal_disc_wild-type [RAL-208]


title: Th2 42 hr Input

status: Public on Sep 20 2012

city: South San Francisco

first: Smita

last: Agrawal

address: 1 DNA Way

department: Immunology

institute: Genentech Inc.

data_processing:
Illumina Casava1.7 software used for basecalling and generating eland extended files mapped onto mm9
Sequenced reads for the BMDCs were mapped to mm9 whole genome using gsnap with parameter s-d mm9 -Q -n 2 -A sam
QuEST was used for peak calling on the aligned eland extended or SAM files with the recommended 30 -fold enrichment used as threshold.
Genome_build: mm9
Supplementary_files_format_and_content: wig files indicating the reads aligned to the mm9 genome

source_name: Th2 polarized cells

extract_protocol: 20000000 cells were harvested, crosslinked with formaldehyde, sonicated, IPed with appropriate antibodies and reverse-crosslinked to obtain 300-500 bp DNA fragments. These DNA fragments were ligated to Illumina TruSeq adapters  for sequencing on the Illumina GAIIx.

tag: cell type/growth condition

value: Naïve T-cells from spleen under Th2 polarizing conditions

tag: timepoint

value: 42 hrs


title: at-endosperm-ler_fie_x_col_wt

description: Arabidopsis thaliana F1-endosperm of fie-1 Landsberg-erecta (male) crossed with Columbia-0 (female).

source_name: AT F1-Endosperm fie-1 Landsberg x Columbia

value: endosperm


title: at-endosperm-ler_wt_x_col_wt

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta (male) crossed with Columbia-0 (female).

source_name: AT F1-Endosperm Landsberg x Columbia


title: at-embryo-col_wt_x_ler_wt

description: Arabidopsis thaliana F1-embryo of Columbia-0 (female) crossed with Landsberg-erecta (male).

source_name: AT F1-Embryo Columbia x Landsberg

value: embryo


title: at-endosperm-col_wt_x_ler_wt

description: Arabidopsis thaliana F1-endosperm of Columbia-0 (female) crossed with Landsberg-erecta (male).

source_name: AT F1-Endosperm Columbia x Landsberg


title: SL2684

city: New York

first: Ashish

last: Agarwal

state: NY

institute: Solvuu

data_processing:
All libraries were sequenced with single-end 36 bp reads on an Illumina GAIIx or single-end 50 bp reads on an Illumina HiSeq 2000
Sequence reads were mapped to the mus musculus genome (version mm9) with Bowtie (version 0.12.7) (Langmead et al., 2009) and with the following settings: -k 1 --best. The --phred33-quals or --phred64-quals parameter was set as needed depending on the format of the input fastq file.
ChIP-seq datasets were further processed to call peaks with the MACS software (version 1.4.0 20110619) using the settings: -p 1e-10 -m 15,30 -s 36 -g mm --bw=200 (Zhang et al., 2008). All were processed against an appropriate control.
RNA-seq datasets were also processed through Tophat (version 1.2.0) with settings: -a 10 -g 20 --no-novel-juncs -G refseqGeneAnnot.gtf (Trapnell et al., 2009).
Tophat results were then pipelined to Cufflinks (version 0.9.3) with the settings: -M 20101217_rRNA_tRNA_mask.gtf -G refseqGeneAnnot.gtf (Trapnell et al., 2010).
Absolute read counts for annotated genomic features were computed using the htseq-count script from the HTSeq (version 0.5.3p3) software suite with parameters: --stranded=no --mode=union.
MACS peaks of multiple TFs were clustered over the genome using a simple R script as described in the accompanying manuscript.
MACS peaks were converted to gene wide scores as decribed in main manuscript
Differential expression analysis for RNA-seq was performed using Deseq with default parameters.
Network inference for RNA-seq compendium was run with the Inferelator with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Each ChIP-Seq dataset includes a result file <lib>_<control>_genes.txt, where the <lib> is the ChIP library and <control> its corresponding control library. This is a MACS output file augmented with additional columns generated by the custom R script described in the data processing steps. Each RNA-Seq dataset includes a result file <lib>_genes.expr.txt, which is the output of cufflinks.

molecule: polyA RNA

source_name: Th2 in vitro

growth_protocol: Naive CD4 T cells were typically cultured under standard non-polarizing Th0 or Th17 differentiation conditions for 48h (or as indicated).

extract_protocol:
RNA was extracted from cells using the Trizol protocol; Transcription factor ChIP/FAIRE-Seq was performed from sonicated, PFA-crosslinked nuclear lysates and for ChIP, TF-DNA complexes were isolated using specific antibodies; Histone ChIP was performed using mono/di-nucleosomes prepared from MNase digested chromatin.
mRNA was prepared from total RNA by poly-A selection and cDNA synthesis was carried out as described (Mortazavi et al., 2008). The resulting dsDNA was prepared for sequencing by ligation of Illumina sequencing adapters, selection of 225 bp fragments from a 2% agarose SizeSelect E-Gel (Invitrogen), and amplification with 15 cycles of PCR using Illumina paired- end primers. Alternatively, some libraries were made using the Nextera tagmentation protocol described (Gertz et al., 2012).

tag: genotype

value: wt

tag: application

value: RNA-Seq


title: SL3306


title: SL6630

source_name: Th17 in vitro

value: Batf wt


title: at-endosperm-col_dme_x_ler_wt

description: Arabidopsis thaliana F1-endosperm of dme-2 Columbia-gl (female) crossed with Landsberg-erecta (male).

source_name: AT F1-Endosperm dme-2 Columbia x Landsberg


title: SL6627


title: SL4029

value: RORg ko


title: SL6631

value: Batf ko


title: SL3320


title: SL3319

value: RORg wt


title: SL3000


title: SL3314

value: B-ATF ko


title: SL2877


title: SL3035


title: SL2999


title: SL2871


title: SL6497


title: SL2876


title: SL3036


title: SL3592


title: SL3593


title: at-embryo-ler_wt_x_col_wt

description: Arabidopsis thaliana F1-embryo of Landsberg-erecta (male) crossed with Columbia-0 (female).

source_name: AT F1-Embryo Landsberg x Columbia


title: SL1943


title: SL1238

value: STAT3 ko


title: SL3782


title: SL1236


title: SL1045

value: IRF4 ko


title: SL972


title: SL1854


title: SL3312

value: c-Maf ko


title: SL1853


title: SL4028


title: SL970


title: SL10567


title: SL9447


title: SL10569


title: SL10566


title: SL7826

value: Batf +/+


title: SL7827

value: Batf -/-


title: SL8357

value: IRF4 wt


title: SL6496

value: Ikzf3 Ikzf3 -/-


title: SL6494

value: Ikzf3 Ikzf3 +/+


title: SL3541

value: STAT3 wt (+/CD4-Cre)


title: SL3310


title: SL4220

value: c-Maf ko (flox/CD4-Cre)


title: SL4218

value: c-Maf wt (+/CD4-Cre)


title: SL4222

value: B-ATF wt (+/+)

value: RNA-Seq


title: SL3308


title: SL4224

value: B-ATF ko (-/-)


title: SL3303


title: SL3301


title: SL2765


title: SL2763


title: SL2680

value: RORg wt (+/+)


title: SL2682

value: RORg ko (GFP KI)


title: SL2675

value: STAT3 ko (flox/CD4-Cre)


title: SL9445


title: SL2775


title: SL2777


title: SL1844


title: SL1858

value: wt


title: SL8347

value: IRF4 ko


title: SL1846


title: SL1850


title: SL1848


title: SL1852


title: SL9858


title: GIS_RnaPet_HeLa-S3_nucleus_longPolyA

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

organism: Homo sapiens

extract_protocol: For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisRnaPet

tag: datatype

value: RnaPet

tag: datatype description

value: RNA Paired-End Tags

tag: rnaextract

value: longPolyA

tag: rnaextract description

value: Poly(A)+ RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: clone-free

tag: readtype

tag: readtype description

value: Paired 36 nt reads

tag: cell sex

value: F

tag: localization

value: nucleus

tag: localization description

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA

tag: replicate


title: SL9625

tag: cell type


title: GIS_RnaPet_HUVEC_cytosol_longPolyA

source_name: HUVEC

value: U

value: cytosol

value: The fluid between the cells outer membrane and the nucleus


title: SL1857

value: RNA-Seq


title: SL1851


title: SL9859


title: SL9623


title: Salt Input

first: Zachary

last: Knight

address: 1230 York Ave

institute: Rockefeller University

data_processing:
SCS-RTA: On-board image analysis
CASAVA v1.8 : Bcl to fastq converstion
Tophat v1.3.1 (Bowtie 0.12.7): Junction mapping/aligning
Cufflinks/Cuffdiff v1.3.0: Transcript assembly/quantitation
Genome build: mm9

source_name: Input RNA

growth_protocol: Wild-type C57Bl/6J mice  were maintained on a 12 hour light-dark cycle and fed ad libitum.

extract_protocol:
Immunoprecipitated and total RNA was purified using the RNAeasy Micro kit.
Clontech SMARTER + Illumina TruSeq RNA-seq

treatment_protocol: Mice  were killed by cervical dislocation at approximately CT6 and hypothalami rapidly dissected.

tag: tissue

value: Hypothalamus

tag: strain

tag: treatment

value: IP injection of 2M NaCl (325 uL) 2h before sacrifice

tag: ps6 antibody


title: Vehicle Input

value: IP injection of PBS (325 uL) 2h before sacrifice


title: SL13421

source_name: Th17 in vitro (RPMI)

tag: genotype

tag: application


title: SL8355

value: wt


title: SL13420


title: SL8353


title: SL1856


title: SL13418


title: SL13419


title: SL1855


title: SL3304

source_name: Th1 in vitro


title: SL13416


title: Salt IP

source_name: pS6 244 immunoprecipitate RNA

value: Cell Signaling #2215 lot 10 + 750 nM 3P phosphopeptide


title: SL10564


title: SL13414


title: SL6634

source_name: Th0 in vitro

value: Batf wt


title: Vehicle IP


title: SL6635

value: Batf ko


title: SL13413


title: SL13412


title: SL3778


title: SL13411


title: SL3190


title: SL13415


title: SL13408


title: F1 EE2

city: Arlington

first: Ye

last: Tian

department: ECE

description: methylation data of E2 treated generation 1

data_processing:
MBDCap-Seq reads were aligned to rn4 genome build using Illumina Casava software
Based on aligned data, count mapped reads of every base pair
Store mapped read count in bedgraph format based on rn4 genome build
Genome_build: rn4
Supplementary_files_format_and_content: bedgraph files were created based on rn4 genome build

organism: Rattus norvegicus

source_name: mammary gland tissue

extract_protocol: Mammary glands were removed, flash frozen on liquid nitrogen.  DNA was extracted using  Wizard Genomic DNA purification kit (promega). Methylated DNA was eluted by the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) according to the manufacturer’s protocol .Methylated DNA was eluted, precipitated and  used for the construction of sequencing libraries.

treatment_protocol: Mammary glands were collected from F1-F3 generation offspring of rat mothers fed either a control of EE2- supplemented diet during pregnancy

value: ethinyl-estradiol

value: mammary gland

tag: generation

tag: genetic background

value: Sprague-Dawley


title: SL13410


title: SL1947


title: F1 control

description: methylation data of control group generation 1

value: control


title: SL13417


title: SL3038


title: SL13406


title: SL13409


title: SL6499


title: SL2683


title: SL4425


title: F2 EE2

description: methylation data of E2 treated generation 2


title: SL13404

value: 24h siInhba; 120309b


title: SL13405


title: SL1234


title: SL13402


title: F2 control

description: methylation data of control group generation 2


title: SL1173


title: SL13403


title: F3 EE2

description: methylation data of E2 treated generation 3


title: SL13398


title: SL13397


title: SL1043


title: SL13399


title: F3 control

description: methylation data of control group generation 3


title: SL2656


title: SL13393


title: SL13394


title: SL13389


title: SL13388

value: 24h siPrkrir;  120309


title: SL13387

value: 24h siPrkrir;  111006


title: SL13390


title: SL9856

value: Batf +/+


title: SL9444

value: IRF4 wt


title: SL9446

value: IRF4 ko


title: SL13384

value: RNA-Seq


title: SL8346


title: SL13401


title: SL9857

value: Batf -/-


title: SL13400


title: SL13385


title: SL13381


title: SL13386


title: SL13383


title: SL8356


title: SL13380


title: SL13379


title: SL13382


title: SL6495

value: Ikzf3 Ikzf3 -/-


title: SL13376


title: SL13375


title: SL13373

value: 24h siNonTarget2; 111029


title: SL4223

value: B-ATF ko (-/-)


title: SL13374

value: 24h siNonTarget2; 120309b


title: SL13378


title: SL4221

value: B-ATF wt (+/+)


title: SL13371

value: 24h siNonTarget2; 111011


title: SL4219

value: c-Maf ko (flox/CD4-Cre)


title: SL13370

value: 24h siNonTarget2; 111006


title: SL13372

value: 24h siNonTarget2; 111014


title: SL13369

value: 24h siNonTarget2; 110930


title: SL11686

value: 24h RPMI siRorc


title: SL3540

value: STAT3 wt (+/CD4-Cre)


title: SL11681


title: SL11684

value: 24h RPMI siJmjd3


title: SL13377


title: SL3307


title: SL11683

value: 24h RPMI Etv6


title: SL11680

value: 24h RPMI siJmjd6


title: SL11685

value: RNA-Seq


title: SL3309


title: SL4217

value: c-Maf wt (+/CD4-Cre)


title: SL11678


title: SL11677

value: 24h RPMI siCntl


title: SL11682


title: SL11679


title: SL3302


title: SL3300


title: SL13873


title: SL13872


title: SL2764


title: SL6493

value: Ikzf3 Ikzf3 +/+


title: SL13869

value: Batf -/-


title: SL2762


title: SL13865

value: Stat3 fl/fl CD4-Cre


title: SL2681

value: RORg ko (GFP KI)


title: SL2679

value: RORg wt (+/+)


title: SL13364

value: wt


title: SL12528

value: Fosl2 +/+ CD4-Cre


title: SL13407


title: SL12366

value: Hif1a fl/fl CD4-Cre


title: SL11894


title: SL13864

value: Stat3 +/+ CD4-Cre


title: SL12530

value: Fosl2 fl/fl CD4-Cre


title: SL2674

value: STAT3 ko (flox/CD4-Cre)


title: SL2774


title: SL14522

value: Batf +/+

value: FAIRE-seq


title: SL11890

value: Hif1a +/+ CD4-Cre


title: SL14523


title: SL2673

value: RNA-Seq


title: SL14527


title: SL14412


title: SL14526


title: SL2776


title: SL14410


title: SL12382


title: SL12364


title: SL13868


title: SL1845


title: SL14406


title: SL1843


title: SL12529


title: SL11896


title: SL12527


title: SL12365

value: Hif1a fl/fl CD4-cre


title: SL11892


title: SL11895


title: SL12363

value: Hif1a +/+ CD4-cre


title: SL2655


title: SL11893


title: SL2654


title: SL1847

value: STAT3 wt (+/CD4-Cre)


title: SL14520


title: SL11889


title: SL14521


title: SL8352


title: SL8354


title: SL2778


title: SL14525

value: Batf -/-


title: SL14411


title: SL14524


title: SL14409


title: SL2653

source_name: media only, naive CD4 T cell

value: naive CD4 T cell


title: SL14407


title: SL3305

source_name: iTreg in vitro

value: iTreg


title: SL2685


title: SL14405


title: SL13871

tag: control

tag: factor

value: ChIP-Seq


title: SL13875


title: SL13874


title: SL3316

value: RORg ko


title: SL11891


title: SL3315

value: RORg wt


title: SL13866


title: SL2875


title: SL14408


title: SL12386

value: wt


title: SL1849


title: SL12384


title: SL2874


title: SL9624


title: SL9626


title: SL1239

value: STAT3 ko


title: SL973


title: SL1944

value: RORg


title: SL13368


title: SL1237


title: SL2870


title: SL3594


title: SL3779


title: SL1042


title: SL3595


title: SL13870


title: SL1948


title: SL13867

value: Stat3 fl/fl CD4-Cre


title: SL1041


title: SL6629

value: Batf ko


title: SL1174


title: SL6628

value: Batf wt


title: SL2873


title: SL3317


title: SL3318


title: SL1040


title: SL971


title: SL1046

value: IRF4 ko


title: SL9854


title: SL3780


title: SL6633


title: SL9855


title: SL9853


title: SL1235


title: SL6632


title: SL10575


title: SL9852

value: Batf +/+


title: SL10572


title: SL4035


title: SL1044


title: SL2994


title: SL4034


title: SL2872


title: SL4032


title: UT-A_ChipSeq_GM13976_Input

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromChip

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: controlid

tag: labversion

value: fseq v 1.84

tag: cell

tag: cell organism

value: human

tag: cell description

value: lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: F

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: UT-A_ChipSeq_GM10248_Input

value: lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12)

tag: cell sex

value: M


title: SL2992

tag: genotype

value: RORg ko

tag: application

value: ChIP-Seq

tag: cell type


title: SL7825

value: Batf -/-

tag: control


title: SL7824

tag: factor


title: UT-A_ChipSeq_Medullo_Input

source_name: Medullo

tag: datatype

value: Medullo

value: medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997)

value: cancer

value: ectoderm

value: U


title: SL2991

value: RORg wt


title: UT-A_ChipSeq_Medullo_CTCF

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_D721

tag: replicate

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: baseAlignCounts.pl v 1


title: UT-A_ChipSeq_GM10248_CTCF

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_GM10248,p-value cutoff:0.05

value: M


title: SL6625

value: wt

value: ChIP-Seq


title: UT-A_ChipSeq_GM10266_Input

value: fseq v 1.84

tag: cell

tag: cell organism

value: human

tag: cell description

value: lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12)

tag: cell karyotype

value: affected

tag: cell lineage

value: mesoderm

tag: antibody

value: Input

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: SL6498

tag: genotype

tag: control

tag: application

tag: cell type


title: UT-A_ChipSeq_Colon_OC_Input

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Primary frozen colon tissue from NCTC donor IDs 10-0005A (Rep B1) and 10-0170A (Rep B2), African American and caucasian

value: normal

tag: cell sex

value: B

tag: antibody description


title: UT-A_ChipSeq_GM13977_Input

value: lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976

value: F


title: UT-A_ChipSeq_LNCaP_androgen_CTCF

source_name: LNCaP

treatment_protocol: androgen

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_LnCAP,p-value cutoff:0.05

tag: replicate

value: M

tag: treatment

value: androgen

tag: treatment description

value: 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford)

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: baseAlignCounts.pl v 1


title: SL3783

value: wt

tag: factor

value: ChIP-Seq


title: SL10573


title: SL3034


title: UT-A_ChipSeq_GM20000_Input

value: ChipSeq

value: Chromatin IP Sequencing

tag: controlid

tag: labversion

value: fseq v 1.84

tag: cell

tag: cell organism

value: human

tag: cell description

value: lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation

tag: cell karyotype

value: affected

tag: cell lineage

value: mesoderm

tag: antibody

value: Input

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: UT-A_ChipSeq_Spleen_OC_CTCF

tag: datatype

tag: datatype description

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_Spleen,p-value cutoff:0.05


title: UT-A_ChipSeq_GM13976_CTCF

tag: antibody antibodydescription

tag: antibody targetdescription

value: fseq v 1.84, iff_GM13976,baseAlignCounts.pl v 1,p-value cutoff:0.05

tag: cell sex

value: F

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF


title: SL3191

tag: genotype

value: wt

tag: control

tag: application

value: ChIP-Seq

tag: cell type


title: UT-A_ChipSeq_Kidney_OC_CTCF

value: ChipSeq

value: Chromatin IP Sequencing

tag: antibody vendorname

tag: antibody vendorid

tag: controlid

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_Kidney,p-value cutoff:0.05

tag: replicate

value: baseAlignCounts.pl v 1


title: SL3781

tag: factor


title: SL2993

value: RORg wt


title: SL4033

value: RORg ko


title: UT-A_ChipSeq_Pancreas_OC_CTCF

tag: labversion

value: fseq v 1.84, iff_Pancreas,baseAlignCounts.pl v 1,p-value cutoff:0.05


title: SL3031

value: c-Maf


title: SL3032


title: SL4424


title: UT-A_ChipSeq_Lung_OC_Input

value: fseq v 1.84

tag: cell

tag: cell organism

value: human

tag: cell description

value: Primary frozen lung tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase) and CF Center donor IDs DD006I (Rep B1 FAIRE) and DD007I (Rep B2 FAIRE)

tag: cell karyotype

value: normal

value: B

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: SL3311

value: c-Maf ko


title: UT-A_ChipSeq_LNCaP_Input

tag: datatype

tag: datatype description

value: LNCaP

value: prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.)

value: cancer

tag: cell lineage

value: endoderm

value: M

tag: antibody


title: SL8351

tag: genotype

value: IRF4 ko

tag: control

value: Batf

tag: application

value: ChIP-Seq


title: SL9451

tag: cell type


title: SL9449

value: IRF4 wt


title: UT-A_ChipSeq_MCF-7_serum_stimulated_media_Pol2

value: ChipSeq

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

tag: controlid

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

tag: cell sex

value: F

tag: treatment

tag: treatment description

value: Grown with normal serum levels (10%), then switched back to normal serum levels (10% FBS) for 3 hours.

value: baseAlignCounts.pl v 1


title: UT-A_ChipSeq_MCF-7_serum_stimulated_media_CTCF

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: labversion

tag: replicate

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF


title: UT-A_ChipSeq_MCF-7_serum_starved_media_CTCF

tag: datatype

tag: datatype description

value: Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours


title: SL6500

value: wt

tag: factor

value: ChIP-Seq


title: SL10570

tag: genotype

value: BATF


title: SL8349

value: IRF4 wt

tag: control

value: Batf


title: UT-A_ChipSeq_LNCaP_CTCF

value: ChipSeq

value: Chromatin IP Sequencing

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_LnCAP,p-value cutoff:0.05

value: M

tag: antibody


title: SL9450

value: IRF4 ko

tag: application

tag: cell type


title: UT-A_ChipSeq_Lung_OC_CTCF

tag: antibody antibodydescription

tag: antibody targetdescription

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_Lung

value: baseAlignCounts.pl v 1


title: UT-A_ChipSeq_Spleen_OC_Input

value: fseq v 1.84

tag: cell

tag: cell organism

value: human

tag: cell description

value: Primary frozen spleen tissue from NICHD donor IDs 1863 (Rep B1) and 4548 (Rep B2)

tag: cell karyotype

value: normal

value: F

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: SL9448

value: ChIP-Seq


title: UT-A_ChipSeq_GM20000_CTCF

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_20000,p-value cutoff:0.05

tag: cell sex

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF


title: SL8348

tag: genotype

value: IRF4 wt

tag: factor

value: Batf


title: UT-A_ChipSeq_Pancreas_OC_Input

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2)

value: M

tag: antibody


title: UT-A_ChipSeq_GM10266_CTCF

tag: antibody antibodydescription

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_GM10266

tag: replicate

value: baseAlignCounts.pl v 1


title: SL8350

value: IRF4 ko

tag: control

tag: application

tag: cell type


title: UT-A_ChipSeq_Kidney_OC_Input

value: fseq v 1.84

tag: cell

tag: cell organism

value: human

tag: cell description

value: Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE)

tag: cell karyotype

value: normal

value: B

value: Input

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: UT-A_ChipSeq_GM13977_CTCF

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: controlid

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_GM13977

value: F

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF


title: UT-A_ChipSeq_MCF-7_serum_stimulated_media_c-Myc

value: ChipSeq

value: Chromatin IP Sequencing

value: Rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:MYC

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

value: Santa Cruz Biotechnology

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

tag: cell sex

tag: treatment

tag: treatment description

value: Grown with normal serum levels (10%), then switched back to normal serum levels (10% FBS) for 3 hours.

value: c-Myc

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:c-Myc

value: Santa Cruz Biotech


title: SL3313

tag: genotype

value: B-ATF ko

tag: factor

value: B-ATF

value: ChIP-Seq


title: SL3037

value: wt

tag: control


title: SL3033

tag: application


title: UT-A_ChipSeq_Heart_OC_Input

tag: datatype

tag: datatype description

value: fseq v 1.84

value: human

value: Primary frozen heart tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B1 FAIRE), 4548 (Rep B2 FAIRE)

value: normal

value: B

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: SL3039

tag: cell type


title: UT-A_ChipSeq_MCF-7_serum_starved_media_c-Myc

value: ChipSeq

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:MYC

tag: antibody targetdescription

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

value: Santa Cruz Biotechnology

tag: replicate

value: F

value: Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours

value: baseAlignCounts.pl v 1


title: SL3192

value: B-ATF

value: ChIP-Seq


title: UT-A_ChipSeq_MCF-7_serum_starved_media_Pol2

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

tag: controlid

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05


title: GIS_RnaPet_IMR90_nucleus_longPolyA

value: RnaPet

value: RNA Paired-End Tags

tag: rnaextract

value: longPolyA

tag: rnaextract description

value: Poly(A)+ RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: clone-free

tag: readtype

tag: readtype description

value: Paired 36 nt reads

tag: localization

value: nucleus

tag: localization description

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: GIS_RnaPet_IMR90_cytosol_longPolyA

tag: datatype

tag: datatype description

value: cytosol

value: The fluid between the cells outer membrane and the nucleus


title: GIS_RnaPet_SK-N-SH_cell_longPolyA

source_name: SK-N-SH

value: cell

value: Whole cell


title: GIS_RnaPet_IMR90_cell_longPolyA


title: GIS_RnaPet_MCF-7_cell_longPolyA

value: iIDR,clone-free

value: iIDR


title: GIS_RnaPet_SK-N-SH_nucleus_longPolyA


title: GIS_RnaPet_SK-N-SH_cytosol_longPolyA


title: GIS_RnaPet_MCF-7_nucleus_longPolyA


title: GIS_RnaPet_A549_cytosol_longPolyA


title: Control leaf

status: Public on Sep 19 2012

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
base-call using Illumina's RTA package
adapter sequence was trimmed by Perl script
smRNA reads were aligned to Arabidopsis TAIR9 genome using C program
read counts are normalized to per million mapped reads
Genome_build: TAIR9
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each smRNA

source_name: Control leaf

growth_protocol: Plants were grown at 22°C with a 150 μmol m-2 S-1 fluorescence rate and under 12 hour/12 hour light dark cycle in MGRL hydroponic medium.

extract_protocol: 3 biological replicates were pooled and total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s protocol. Small RNAs (18 to 28 nt) from 40 μg total RNA were separated and then fractionated using 15% polyacrylamide urea gel. Subsequent steps were carried out by the protocol of Digital Gene Expression for Small RNA Sample Preparation (Illumina). Qualities and quantities of individual sRNA libraries were confirmed using Bioanalyzer.

treatment_protocol: Thirty-day-old plants were subjected to high osmotic stress by adding 0.3M mannitol to the basal MGRL medium for 3 hr in the light.

tag: tissue

value: leaf


title: Euglycemia-cancer cells_FAIRE

city: Dallas

first: Thomas

middle: Nathan

last: Person

state: Texas

address: 5323 Harry Hines Blvd

department: Clinical Sciences

institute: UT Southwestern

description: FAIRE-seq; enriched for soluble chromatin by FAIRE

data_processing:
Basecalling; Bioscope with default parameters
Alignment; Bioscope with default parameters, uniquely mapped 25 bp seed with two mismatches were selected
Peakcalling; MACS(1.4.0beta) with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: peak calling files are in BED format

source_name: Cancer cells isolated from MMTV-PyMT mice_Control-FAIRE

growth_protocol: Freshly isolated cancer cells were cultured with DMEM supplemented with 10% Fetal bovine serum

extract_protocol: FAIRE as described by Giresi et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research, 2007.

treatment_protocol: No treatment

tag: strain background

value: FVB

tag: genotype/variation

value: MMTV-PyMT

tag: cell type

value: Euglycemia (Control)-cancer cells


title: Osmotic root

source_name: Osmotic root

value: root


title: Hyperglycemia-cancer cells _FAIRE

source_name: Cancer cells isolated from MMTV-PyMT/PANIC_HyG-FAIRE

value: Hyperglycemia (HyG)-cancer cells


title: Hyperglycemia-cancer cells_input

description: FAIRE-seq; input DNA

source_name: Cancer cells isolated from MMTV-PyMT/PANIC_HyG-input


title: Control root

source_name: Control root


title: GIS_RnaPet_A549_cell_longPolyA

value: RnaPet

value: RNA Paired-End Tags

value: longPolyA

value: Poly(A)+ RNA longer than 200 nt

tag: replicate


title: GIS_RnaPet_A549_nucleus_longPolyA

value: clone-free

value: Paired 36 nt reads

value: nucleus

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: DPN 48h - Adenoma 4

city: Solna

first: Mikael

last: Huss

address: Tomtebodav. 23A

country: Sweden

institute: Science for Life Laboratory Stockholm

description: Sample 22

data_processing:
Base-calling was done with Illumina's Offline Base Caller (OLB) v.1.9.
Alignment to reference genome was done with TopHat v1.0.14.
Duplicates were removed using Picard (v. 1.29) MarkDuplicates.
Read counts per gene were calculated with HTSeq v. 0.5.1.
FPKM values for genes and transcripts were calculated with Cufflinks v. 1.0.3.
Differential expression analysis was performed using the edgeR package and subsequent custom filtering
Genome_build: hg19
Supplementary_files_format_and_content: count_table.txt:  tab separated text file (read counts per ENSEMBL gene)
Supplementary_files_format_and_content: fpkm_table.txt: tab separated text file (FPKM per ENSEMBL gene)

source_name: Parathyroid adenoma

growth_protocol: Tissue for cell culturing was obtained from four parathyroid adenomas collected directly at surgery. All samples were from female, postmenopausal patients with chief cell adenoma with no preoperative signs of malignancy or kidney failure. Isolation of cells and cell culturing were performed essentially as previously described by Lu et al. In brief, tissues were cut and digested into cells with 1.5 mg/mL collagenase type II. About 1×106 cells were plated

extract_protocol: Illumina TruSeq RNA

treatment_protocol: cells were plated and treated with 100 nM DPN (Tocris Bioscience), or 100 nM OHT (Sigma-Aldrich, Stockholm, Sweden) for 24h or 48h, respectively. Untreated cells cultured in parallel were used as controls.

tag: patient

value: Parathyroid tumor

tag: agent

value: DPN

tag: time


title: OHT 48h - Adenoma 4

description: Sample 24

value: OHT


title: DPN 24h - Adenoma 4

description: Sample 21


title: Control 48h - Adenoma 4

description: Sample 20

value: Control


title: OHT 48h - Adenoma 3

description: Sample 18


title: OHT 24h - Adenoma 3

description: Sample 17


title: DPN 48h - Adenoma 3

description: Sample 16


title: Osmotic leaf

source_name: Osmotic leaf

value: leaf


title: GIS_RnaPet_MCF-7_cytosol_longPolyA

tag: rnaextract

tag: rnaextract description

tag: biorep

value: cytosol

value: The fluid between the cells outer membrane and the nucleus


title: Control 48h - Adenoma 3

description: Sample 14


title: Euglycemia-cancer cells_input

description: FAIRE-seq; input DNA

source_name: Cancer cells isolated from MMTV-PyMT mice_Control-input

value: FVB

value: MMTV-PyMT

value: Euglycemia (Control)-cancer cells


title: DPN 24h - Adenoma 3

description: Sample 15


title: Control 24h - Adenoma 3

description: Sample 13


title: UW_DnaseDgf_TReg-Activated_adult-8wks

source_name: TReg-Activated

extract_protocol: For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeUwDgf

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

tag: cell

value: TReg-Activated

tag: cell organism

value: mouse

tag: cell description

value: Activated primary T regulatory cells, isolated ex vivo

tag: cell sex

value: M

tag: age

tag: age description

value: Adult 8 weeks

tag: labexpid

tag: labversion

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: OHT 48h - Adenoma 2

description: Sample 12

tag: patient

tag: tissue

value: Parathyroid tumor

tag: agent

value: OHT


title: OHT 24h - Adenoma 2

description: Sample 11

tag: time


title: DPN 48h - Adenoma 2

description: Sample 10

value: DPN


title: UW_DnaseDgf_THelper-Activated_adult-8wks

source_name: THelper-Activated

tag: datatype

tag: datatype description

value: THelper-Activated

value: Activated primary CD4 effector cells, isolated ex vivo

tag: replicate


title: Control 24h - Adenoma 2

description: Sample 7

value: Control


title: UW_DnaseDgf_Retina_newborn-1days

source_name: Retina

tag: lab

tag: lab description

tag: cell

value: Retina

value: Newborn 1 day


title: Control 48h - Adenoma 2

description: Sample 8


title: UW_DnaseDgf_A20_immortalized

value: UW-m

value: Stamatoyannopoulous - University of Washington

tag: cell organism

tag: cell description

value: B cell lymphoma line derived from a spontaneous reticulum cell neoplasm

tag: cell sex

value: immortalized

value: Immortal cells

value: BALB/cAnN

value: ccMyeloma high incidence H2d


title: UW_DnaseDgf_NIH-3T3_immortalized

value: DnaseDgf

value: DNase Digital Footprinting

value: mouse

value: fibroblast

value: M

tag: age

tag: age description

tag: labexpid

value: NIH/Swiss

value: An outbred Swiss mouse  used as a general-purpose stock. Used extensively for pertussis HSF testing.


title: OHT 48h - Adenoma 1

description: Sample 6

value: Parathyroid tumor

value: OHT


title: UW_DnaseDgf_WholeBrain_E14.5

source_name: WholeBrain

value: WholeBrain

value: Whole Brain

value: Embryonic day 14.5

tag: labversion

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: UW_DnaseDgf_ES-CJ7_E0

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.)

value: Embryonic day 0 (stem cell)

value: Control inbred strain of the steel-derived ES cells.


title: OHT 24h - Adenoma 1

description: Sample 5

tag: patient

tag: tissue

tag: agent


title: UW_DnaseDgf_T-Naive_adult-8wks

source_name: T-Naive

tag: datatype

value: DnaseDgf

tag: datatype description

value: DNase Digital Footprinting

value: T-Naive

value: Naive T cells:CD4+, CD25-

value: Adult 8 weeks


title: DPN 24h - Adenoma 1

description: Sample 3

value: DPN

tag: time


title: UW_DnaseDgf_MEL_immortalized

source_name: MEL

tag: lab

tag: lab description

value: MEL

value: mouse

value: Leukemia (K562 analog)

value: M

value: immortalized

value: Immortal cells

tag: replicate

value: Unknown

value: Unknown strain origin


title: Control 48h - Adenoma 1

description: Sample 2

value: Parathyroid tumor

value: Control


title: UW_DnaseDgf_ZhBTc4_E0_DS17616

value: UW-m

value: Stamatoyannopoulous - University of Washington

tag: cell

tag: cell organism

tag: cell description

value: Undifferentiated mouse embryonic stem cells

value: Embryonic day 0 (stem cell)

value: The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice.


title: Control 24h - Adenoma 1

description: Sample 1


title: UW_DnaseDgf_Heart_adult-8wks

source_name: Heart

value: DnaseDgf

value: DNase Digital Footprinting

value: Heart

tag: cell sex

tag: age

tag: age description

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse


title: OHT 24h - Adenoma 4

description: Sample 23

value: OHT


title: UW_DnaseDgf_ZhBTc4_E0_DS17562

value: mouse

value: M

tag: labexpid

tag: labversion

tag: strain


title: UW_DnaseDgf_Kidney_adult-8wks

source_name: Kidney

value: Kidney

tag: strain description


title: DPN 24h - Adenoma 2

description: Sample 9

tag: patient

tag: tissue

tag: agent

value: DPN


title: UW_DnaseDgf_Lung_adult-8wks

source_name: Lung

tag: datatype

tag: datatype description

value: Lung


title: UW_DnaseDgf_Thymus_adult-8wks

source_name: Thymus

tag: lab

tag: lab description

value: Thymus


title: UW_DnaseDgf_B-cell_(CD43-)_adult-8wks

description: SRR574026, which is associated with SRX188640/GSM1003813, and SRR579076, which is associated with SRX191028/GSM1014170, are the same runs.

value: UW-m

tag: cell

value: mouse spleen B cells, CD43-,CD11b-

tag: replicate


title: UW_DnaseDgf_416B_immortalized

value: Stamatoyannopoulous - University of Washington

tag: cell organism

tag: cell description

value: myeloid progenitor cells, CD34+

value: immortalized

value: Immortal cells

value: Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1.


title: UW_DnaseDgf_TReg_adult-8wks

source_name: TReg

value: DnaseDgf

value: DNase Digital Footprinting

value: TReg

value: Regulatory T cells CD4+,CD25+

tag: cell sex

tag: age


title: UW_DnaseDgf_3134_immortalized

value: mouse

value: Mammary

tag: age description

tag: labexpid

value: RIII

value: High mammary tumor incidence in unfostered substrains.


title: Snyder EGL-5 Input L3 replicate 2

status: Public on Sep 18 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

organism: Caenorhabditis elegans

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

tag: strain

value: OP54(official name :OP54 genotype :unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by :R. Waterston and S. Kim )

tag: developmental stage

tag: genotype

tag: Sex

value: Hermaphrodite


title: DPN 48h - Adenoma 1

description: Sample 4

tag: patient

tag: tissue

value: Parathyroid tumor

tag: agent

value: DPN

tag: time


title: Unstimulated macrophages Foxo3a Wildtype ChIP-Seq

city: Seattle

first: Ayush

last: Raman

state: WA

address: 401 Terry Avenue North

department: Computational Dept.

institute: Institute for Systems Biology

data_processing:
ChIP-Seq data was aligned to the mouse genome (NCBI37/mm9; July 2007) using the ELAND alignment software (Illumina). Regions where the ChIP signals were enriched relative to the normal rabbit serum (NRS) control. We have used our in-house pipeline. The peak was identiﬁed as a binding location if and only if all the three conditions were simultaneously satisﬁed: i) the ChIP-Seq signal in the TF-speciﬁc IP/H4Ac was at least ﬁve times the control ChIP-Seq signal (ii) the ChIP-Seq signal in the TF-speciﬁc IP/H4Ac was at least two fragments per million; and (iii) the ChIP-Seq signal in the TF-speciﬁc IP/H4Ac corresponded to at least six overlapping fragments (extended reads) at that peak.
Reference: Ramsey,S.A. et al. Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics 26, 2071-2075 (2010).

*export.txt: ELAND file
*bed: BED file obtained by converting the ELAND file
*bar: BAR file obtained by converting the processed data files; Tags per million; Used for visualizing in the Integrated Genome Browser (IGB)

Genome Build:
Foxo3_BMM_export.txt: NCBI37/mm9 (July 2007)
Foxo3_BMM.bed: NCBI37/mm9 (July 2007)
Foxo3_BMM.tpm.bar: NCBI37/mm9 (July 2007)

source_name: Unstimulated macrophages, wildtype, Foxo3a ChIP

extract_protocol: For ChIP-Seq analysis, formalin-fixed cells were sonicated and processed for immunoprecipitation. Briefly, 1.5 X 10^7 BMMs were crosslinked for 10 min. in 1% paraformaldehyde, washed and lysed. Chromatin was sheared by sonication (5 x 60 s at 30% maximum potency) to fragments of approximately 150bp. The sheared chromatin was incubated with anti-rabbit IgG Dynabeads (Invitrogen) pre-conjugated with antibodies to FOXO3 (H-144) or H4Ac, washed and eluted. The eluted chromatin was reverse-cross-linked, and DNA was purified using phenol/chloroform/isoamyl extraction. The purified ChIP DNA was prepared for sequencing with the Illumina ChIPSeq Sample Prep kit and processed in according to the manufacturer’s protocol. Sequencing was performed by Covance, Seattle, WA.

tag: background strain

value: wildtype

tag: cell type

value: unstimulated bone marrow macrophages

tag: chip antibody

value: anti-Foxo3a (FKHRL1 (H-144))

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody catalog #

tag: antibody lot#


title: UW_DnaseDgf_B-cell_(CD19+)_adult-8wks

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: B Cell , CD19+

tag: cell sex

value: M

tag: age

value: Adult 8 weeks

tag: labversion

tag: replicate

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: Snyder EGL-5 Input L3 replicate 1

description: input DNA

tag: strain

tag: developmental stage

tag: genotype

value: unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG]

tag: Sex


title: Unstimulated macrophages H4Ac Wildtype ChIP-Seq

data_processing:
ChIP-Seq data was aligned to the mouse genome (NCBI37/mm9; July 2007) using the ELAND alignment software (Illumina). Regions where the ChIP signals were enriched relative to the normal rabbit serum (NRS) control. We have used our in-house pipeline. The peak was identiﬁed as a binding location if and only if all the three conditions were simultaneously satisﬁed: i) the ChIP-Seq signal in the TF-speciﬁc IP/H4Ac was at least ﬁve times the control ChIP-Seq signal (ii) the ChIP-Seq signal in the TF-speciﬁc IP/H4Ac was at least two fragments per million; and (iii) the ChIP-Seq signal in the TF-speciﬁc IP/H4Ac corresponded to at least six overlapping fragments (extended reads) at that peak.
Reference: Ramsey,S.A. et al. Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics 26, 2071-2075 (2010).

*export.txt: ELAND file
*bed: BED file obtained by converting the ELAND file
*bar: BAR file obtained by converting the processed data files; Tags per million; Used for visualizing in the Integrated Genome Browser (IGB)

Genome Build:
H4Ac_WT_BMM_export.txt: NCBI37/mm9 (July 2007)
H4Ac_WT_BMM.bed: NCBI37/mm9 (July 2007)
H4Ac_WT_BMM.tpm.bar: NCBI37/mm9 (July 2007)

source_name: Unstimulated macrophages, wildtype, H4Ac ChIP

tag: background strain

tag: cell type

tag: chip antibody

value: anti-H4Ac (anti-acetyl-histone H4)

tag: antibody vendor

value: Upstate Biotechnology

tag: antibody catalog #

tag: antibody lot#


title: UW_DnaseDgf_WholeBrain_adult-8wks

tag: lab

tag: lab description

tag: datatype

value: DnaseDgf

tag: datatype description

value: DNase Digital Footprinting

tag: cell

value: WholeBrain

tag: cell organism

value: mouse

value: Whole Brain

tag: age description

tag: labexpid


title: Snyder EGL-5 POL-2 L3 replicate 1

description: ChIP DNA; Antibody information listed below: official name: Covance 8WG16:MMS-126R;target name: RNA Polymerase II;host: Mouse;antigen: 8WG16;clonal: Monoclonal;purified: Affinity;company: Covance;catalog: MMS-126R;short description: The recognizes the C terminal heptapeptide repeat present on the largest unit of POL II.

tag: strain

value: OP54(official name :OP54 genotype :unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by :R. Waterston and S. Kim )

tag: developmental stage

value: Hermaphrodite


title: IRF4KO CD4 T +IL21 RNASeq

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: treated IL-21

data_processing:
For ChIP-Seq, Basecalls performed using CASAVA version 1.4 (Genome analyzer), 1.7 (GAII) and 1.8 (GAII and HiSeq2000); For RNA-Seq, Basecalls performed using CASAVA version 1.7 (Genome Analyzer) and 1.8 (HiSeq2000)
ChIP-Seq reads were aligned to the mm8 genome assembly using CASAVA pipeline 1.4, 1.7 and Bowtie 0.12.4
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts
For ChIP-Seq, peaks are called using MACS 1.3.7.1; For RNA-Seq, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using mm8 refseq database
Genome_build: mm8
Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.4, 1.7 and unpublished python scripts, rpkm (abundance measurement) files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts

source_name: CD4+ T Cells

growth_protocol: For RNA-Seq, total RNA was extracted from 5x10^6 cells per sample using Rneasy Mini kit (QIAGEN) and the quality and concentration were determined by Nanodrop ND-1000 spectrophotometer. Double-stranded cDNA was synthesized using random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (all from Invitrogen) and fragmented using Bioraptor. After repairing ends, adaptor (Illumina) was added using T4 DNA ligase (New England Biolabs), and 220-400 bp fragments were isolated using 2% E-Gel (Invitrogen) and amplified for 17 cycles using PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs).

extract_protocol: For RNA-Seq, Double-stranded cDNA was synthesized using random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (all from Invitrogen) and fragmented using Bioraptor.

treatment_protocol: not treated or treated by IL-21 (100 ng/ml) for 1 hr

value: CD4+ T Cells

tag: tissue

value: Spleen

tag: treatment

value: treated IL-21


title: UW_DnaseDgf_Liver_adult-8wks

source_name: Liver

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: Liver

tag: cell description

tag: cell sex

tag: age

tag: labversion

tag: replicate

tag: strain description


title: Snyder EOR-1 Input L3 replicate 2

description: input DNA

value: OP54(official name :OP54 genotype :unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by :R. Waterston and S. Kim )

tag: genotype

tag: Sex


title: Snyder EGL-5 POL-2 L3 replicate 2

value: unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG]


title: BB_Input_ChIP-seq

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

data_processing:
Basecalls performed using the CASAVA software
ChIP-seq reads were aligned to the mm9 genome assembly using the BWA program (Li et al, Bioinformatics)
Peaks were called using HOMER with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph and bed files generated by HOMER

source_name: Mammary tissues

extract_protocol:
Frozen-stored mammary tissues were broken into powder with mortar and pestle and then cross-linked with 1% formaldehyde for 10 min, and their nuclei were fractionated by sucrose density gradient centrifugation.  Chromatin was fragmented to 200 to 300 bp by sonication.  Antibodies against STAT5A (# sc-1081, Santa Cruz, CA), STAT5B (# sc-835, Santa Cruz), RNA polymerase II (# ab5408, Abcam), and histone H3K4me3 (# 17-614, Millipore, Temecula, CA) were used for ChIP.
The ChIP DNA fragments were blunt-ended and ligated to the Illumina Indexed DNA adaptors using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (# E6240, New England BioLabs, Ipswich, MA), and sequenced using the Illumina HiSeq 2000.

tag: chip antibody

value: Day of parturition


title: IRF4KO CD4 T -IL21 RNASeq

description: non-treated

tag: cell type

value: non-treated


title: WT CD4 T +IL21 RNASeq

description: treated IL-21


title: Unstimulated macrophages H4Ac Foxo3 Knockout ChIP-Seq

data_processing:
ChIP-Seq data was aligned to the mouse genome (NCBI37/mm9; July 2007) using the ELAND alignment software (Illumina). Regions where the ChIP signals were enriched relative to the normal rabbit serum (NRS) control. We have used our in-house pipeline. The peak was identiﬁed as a binding location if and only if all the three conditions were simultaneously satisﬁed: i) the ChIP-Seq signal in the TF-speciﬁc IP/H4Ac was at least ﬁve times the control ChIP-Seq signal (ii) the ChIP-Seq signal in the TF-speciﬁc IP/H4Ac was at least two fragments per million; and (iii) the ChIP-Seq signal in the TF-speciﬁc IP/H4Ac corresponded to at least six overlapping fragments (extended reads) at that peak.
Reference: Ramsey,S.A. et al. Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics 26, 2071-2075 (2010).

*export.txt: ELAND file
*bed: BED file obtained by converting the ELAND file
*bar: BAR file obtained by converting the processed data files; Tags per million; Used for visualizing in the Integrated Genome Browser (IGB)

Genome Build:
H4Ac_FoxoNull_BMM_export.txt: NCBI37/mm9 (July 2007)
H4Ac_FoxoNull_BMM.bed: NCBI37/mm9 (July 2007)
H4Ac_Foxo3Null_BMM.tpm.bar: NCBI37/mm9 (July 2007)

source_name: Unstimulated macrophages, Foxo3 knockout, H4Ac ChIP

tag: background strain

value: Foxo3a knockout

value: unstimulated bone marrow macrophages

value: anti-H4Ac (anti-acetyl-histone H4)

tag: antibody vendor

value: Upstate Biotechnology

tag: antibody catalog #

tag: antibody lot#


title: WT CD4 T -IL21 RNASeq

description: non-treated

tag: strain


title: IRF4KO CD4 T +IL21 cJun

description: Chromatin IP against Pan-JUN

growth_protocol: For ChIP-Seq, T and B cells were isolated using kits (Miltenyi). Cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum. For pre-activation, cells were stimulated with plate-bound anti-CD3 (2 ug/ml) + anti-CD28 (1 ug/ml) for 3 days, washed, rested overnight.

extract_protocol: For ChIP-Seq, chromatin was prepared from cells cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication and the ChIP DNA was blunt-ended, ligated to the Solexa adaptor and amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols.

treatment_protocol: not treated or treated with IL-21 (100 ng/ml) for 1 hr

tag: tissue


title: Snyder EOR-1 POL-2 L3 replicate 1

tag: developmental stage


title: BB_H3K4me3_ChIP-seq

value: histone H3K4me3

tag: antibody vendor/catalog#

value: Millipore, Temecula, 17-614


title: IRF4KO CD4 T +IL21 IRF4

description: Chromatin IP against IRF4

value: IRF4 (Santa Cruz, sc-6059, k1209)


title: BB_PolII_ChIP-seq

value: RNA polymerase II

value: Abcam, ab5408


title: WT CD4 T +IL21 STAT3

description: Chromatin IP against STAT3

value: CD4+ T Cells

value: Spleen

value: STAT3 (Invitrogen, 13-7000)


title: WT CD4 T +IL21 panJun

description: Chromatin IP against Pan-JUN


title: BB_STAT5A_ChIP-seq

value: Santa Cruz, sc-1081


title: WT CD4 T +IL21 IRF8

description: Chromatin IP against IRF8

value: IRF8 (from Keiko Ozato, not commercial available)


title: BB_STAT5B_ChIP-seq

value: Santa Cruz, sc-835


title: WT CD4 T -IL21 panJun

description: Chromatin IP against Pan-JUN


title: WT CD4 T +IL21 IRF4

description: Chromatin IP against IRF4


title: WT CD4 T -IL21 STAT3

description: Chromatin IP against STAT3


title: AABB_Input_ChIP-seq

value: Day of parturition


title: AABB_H3K4me3_ChIP-seq


title: WT CD4 T -IL21 IRF8

description: Chromatin IP against IRF8


title: Snyder EOR-1 POL-2 L3 replicate 2

value: OP54(official name :OP54 genotype :unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by :R. Waterston and S. Kim )

value: Hermaphrodite


title: WT CD4 T IgG

description: Chromatin IP against IgG

value: Rabbit IgG (R&D, AB-105-C, ER11)


title: AABB_PolII_ChIP-seq


title: Snyder EOR-1 Input L3 replicate 1

description: input DNA

value: unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG]


title: Day 5 differentiated H1 derived VE-cadherin+CD73-CD43lowCD235a+CD41a-CD117- cells [duplicate_2of2]

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

institute: University of Wisconsin

data_processing:
Samples were loaded on the flowcell cluster station. The Genome Analyzer II recipe was used. The runs were single-readed. Image analysis and base calling were done with The Illumina Genome Analyzer Pipeline Software.
After quality assessment and adaptor filtering, the raw sequencing reads were then aligned to the annotated 31,147 non-ribosomal, non-mitochondrial RefSeq genes (Human hg18 or NCBI36 build) using the Bowtie algorithm by allowing two mismatches [1]. At most 200 alignments were allowed if a read maps to multiple genes (gene multireads) or maps to a single gene but multiple isoforms (isoform multiplereads). Isoform or gene relative expression level was estimated and quantified by rsem algorithm in terms of "transcripts per million" (tpm) [2].
Genome_build: hg18
Supplementary_files_format_and_content: txt files reporting tpm values and expected counts.
1. Ben Langmead, Cole Trapnell, Mihai Pop and Steven L Salzberg. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.  Genome Biology 2009, 10:R25
2. B. Li, V. Ruotti, R. Stewart, J. Thomson, and C. Dewey (2010). RNA-Seq gene expression estimation with read mapping uncertainty.   Bioinformatics 26(4): 493-500.

source_name: H1 differentiated on OP9

growth_protocol: H1 cells were differentiated on OP9 stromal cells for 5 days in a medium containing alpha-MEM/, 10% FBS, 100mM monothioglycerol and 50mg/ml ascorbic acid solutions

extract_protocol: Differentiated H1 cells were sorted by MACS and FACS and total RNA was isolated from each cell subset using RiboPure kit (Ambion). Poly A+ RNAs were linearly amplified using a modified T7 amplification method (Sengupta etal, 2010) to generate highly consistent, strand specific mRNA-Seq libraries. After the cDNA libraries were constructed, the samples were quantified with Qubit fluorometer (Invitorgen) and were then sequenced for 42 cycles of single read sequencing on the Illumina Genome Analyzer Pipeline Software..

treatment_protocol: Following differentiation cells were sorted byMACS and  FACS and RNA was isolated using Ambion RiboPure kit. Briefly cells were lysed in TRI-reagent and 100ul of BCP was added, following 10mins of incubation at room temperature cells were centrifuged at 10,000rpm for 15 mins. Aqueous layer was collected and 200 ul of isopropanol was added and cells were centrifuged at 10,000rpm for 15mins. Further pellet was rinsed with 70% ethanol and dissolved in RNase free water.

tag: antibody used for sorting

value: CD31 (BD Biosciences 555445), CD43 (BD Biosciences 555475), CD41a (BD Biosciences 555467), CD73(BD Biosciences 550257), CD144(BD Biosciences 560411), CD235a (BD Biosciences 555570)

value: Angiogenic hematopoietic progenitors


title: AABB_STAT5B_ChIP-seq


title: Day 5 differentiated H1 derived VE-cadherin+CD73+CD235a/CD43-CD117high cells

value: Non-hemogenic endothelial progenitors


title: H1 derived endothelial cells at passage 2

growth_protocol: H1 derived CD31+ endothelial cells were grown in Human endothelial serum free medium (ESFM) (Invitrogen) on fibronectin coated plates

value: H1 derived endothelial cells


title: Undifferentiated H1

source_name: H1 undifferentiated

growth_protocol: Undifferentiated H1 cells were maintained on MEFs in a medium containing DMEM/F12, 100mM L-glutamine/2-mercaptoethanol, 20% knockout serum, 1X non-essential aminoacids and 4ng/ml bFGF2

value: H1 hESCs undifferentiated


title: Day 5 differentiated H1 derived VE-cadherin+CD73-CD235a/CD43-CD117intermediate cells

value: Hemogenic endothelial progenitors


title: WT pre-B cells RNASeq

description: non-treated

source_name: B cells

value: B cells

value: Bone Marrow

tag: treatment

value: non-treated


title: WT pro-B cells RNASeq

description: non-treated


title: AABB_STAT5A_ChIP-seq

value: Santa Cruz, sc-1081


title: Day 4 differentiated H1 derived KDRbright VE-cadherin+ cells

growth_protocol: H1 cells were differentiated on OP9 stromal cells for 4 days in a medium containing alpha-MEM/, 10% FBS, 100mM monothioglycerol and 50mg/ml ascorbic acid solutions

value: Anti-human KDR-PE (R&D Systems, cat#FAB357P); Anti-human CD31-FITC (BD Biosciences; cat#555445) CD144-FITC (BD bioscience; cat#560411)

value: Pan-endothelial progenitors


title: Human umbelical vein endothelial cells derived RNA

source_name: Human umbelical vein endothelial cells

growth_protocol: HUVEC RNA was purchased from Cell Applications, INC.

value: Human umbelical vein endothelial cells


title: Day 4 differentiated H1 (human embryonic stem cell) derived EMHlin-KDRbrightAPLNR+PDGFRalow/- cells [duplicate_2of2]

value: Hematovascular Mesodermal Precursors/Direct Precursors of Hemogenic Endothelium


title: Treg RNASeq

description: 2x polarized

source_name: Treg Cells

value: Treg Cells

value: Spleen

value: 2x polarized


title: Day 8 differentiated H1 derived lin-CD34+CD43+CD235a/CD41a-CD45+ cells

growth_protocol: H1 cells were differentiated on OP9 stromal cells for 8 days in a medium containing alpha-MEM/, 10% FBS, 100mM monothioglycerol and 50mg/ml ascorbic acid solutions

value: CD43 (BD Biosciences 555475), CD45(BD Biosciences 555485), CD41a (BD Biosciences 555467), CD235a (BD Biosciences 555570)

value: lin-CD34+CD43+CD45+CD38- multipotent hematopoietic progeniotrs


title: Day 8 differentiated H1 derived lin-CD34+CD43+CD235a/CD41a-CD45- cells

growth_protocol: H1 cells were differentiated on OP9 stromal cells for 8 in a medium containing alpha-MEM/, 10% FBS, 100mM monothioglycerol and 50mg/ml ascorbic acid solutions

value: lin-CD34+CD43+CD45-CD38- multipotent hematopoietic progeniotrs


title: Day 8 differentiated H1 derived CD34+CD43+CD235a/CD41a+CD45- cells

value: Hematopoietic cells enriched in erythro-megakaryocytic progenitors


title: Day 3 differentiated H1 derived endothelial cores from hemangioblast colonies

growth_protocol: H1 cells were differentiated on OP9 stromal cells for 3 days in a medium containing alpha-MEM/, 10% FBS, 100mM monothioglycerol and 50mg/ml ascorbic acid solutions. APLNR+PDGFRA+ cells were sorted and plated on semi solid methyl cellulose medium containing bFGF to form endothelial  cores for 3 days.

value: Endothelial intermediates formed during development of hemangioblast colonies in semisolid medium


title: Th2 RNASeq

description: 2x polarized

source_name: Th2 Cells

value: Th2 Cells


title: Day 5 differentiated H1 derived VE-cadherin+CD73-CD43lowCD235a+CD41a-CD117- cells [duplicate_1of2]

value: CD31 (BD Biosciences 555445), CD43 (BD Biosciences 555475), CD41a (BD Biosciences 555467), CD73(BD Biosciences 550257), CD144(BD Biosciences 560411), CD235a (BD Biosciences 555570)

value: Angiogenic hematopoietic progeniotrs


title: Th1 RNASeq

description: 2x polarized

source_name: Th1 Cells

value: Th1 Cells


title: Day 5 differentiated H1 derived VE-cadherin+CD73-CD43+CD235a+CD41a+ cells


title: Day 4 differentiated H1 derived KDRdim cells

value: Mesodermal subset without hematopoietic potential


title: Day 4 differentiated H1 (human embryonic stem cell) derived EMHlin-KDRbrightAPLNR+PDGFRalow/- cells [duplicate_1of2]

value: Anti-human KDR-PE (R&D Systems, cat#FAB357P); Anti-human CD31-FITC (BD Biosciences; cat#555445) CD144-FITC (BD bioscience; cat#560411)


title: Th9 RNASeq

description: 2x polarized

source_name: Th9 Cells

extract_protocol: For RNA-Seq, For RNA-Seq, Double-stranded cDNA was synthesized using random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (all from Invitrogen) and fragmented using Bioraptor..

value: Th9 Cells


title: Th17 Stat3

description: Chromatin IP against STAT3

source_name: Th17 Cells

value: Th17 Cells

value: STAT3 (Invitrogen, 13-7000)


title: Th17 JunD

description: Chromatin IP against JunD

value: JunD (Santa Cruz, sc-74, J-1411)


title: Th17 IRF4

description: Chromatin IP against IRF4

value: Spleen

value: IRF4 (Santa Cruz, sc-6059, k1209)


title: Th17 cJun

description: Chromatin IP against cJun


title: WT CD4 T -IL21 IRF4

description: Chromatin IP against IRF4

value: CD4+ T Cells


title: MeDIP_A2058 TET2 cells

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

country: China

institute: Fudan Univ, Shanghai, China

description:
Melanoma cell line A2058 overexpressing full-length wild type human TET2.
MeDIPed genomic DNA.

data_processing:
Basecalls performed using CASAVA version 1.8.2.
MeDIP-Seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with unique map and other default parameters to obtain alignments in SAM format.
SAM alignments were converted into BAM format using samtools(v0.1.18(r982:295)).
BAM alignments were converted to BED format using bedtools.
An in-house program was used to remove duplicated reads generated by PCR in the sequencing library, and to extend 300bp based on the strand that is aligned to because the gels for sequencing are cut at about 200-400bp.
Genome_build: hg19
Supplementary_files_format_and_content: BED format.

source_name: A2058, TET2, MeDIP

growth_protocol: Benign nevus and melanoma tissues were isolated from patients. A2058 MOCK, A2058 TET2 and A2058 TET2M cells were cultured with complete DMEM medium.

extract_protocol: Genomic DNA of human melanoma, nevus and human melanoma cell lines (A2058 MOCK, A2058 TET2, A2058 TET2 M) was purified using the Qiagen Blood & Cell Culture DNA Mini Kit (Cat. No: 13323) and sonicated. Illumina barcode adapters were ligated before hMeDIP. Adaptor-ligated DNA (5 μg) was denatured and incubated with 3 μl of 5-hmC antibody (Active Motif) or 5 μg of 5-mC antibody (Eurogentec) at 4°C overnight. Antibody-DNA complexes were captured by protein A/G beads. The immunoprecipitated DNA was purified and sequenced following standard Illumina protocols.

tag: cell line

value: melanoma cells

tag: overexpression

value: full-length catalytically inactive human TET2 mutant

tag: ip antibody

value: Eurogentec

tag: catalog #

tag: lot#


title: MeDIP_A2058 Mock cells

description:
Melanoma cell line A2058 overexpressing empty vector.
MeDIPed genomic DNA.

source_name: A2058, mock, MeDIP

value: full-length wild type human TET2


title: Th17 JunB

description: Chromatin IP against JunB

tag: chip antibody

value: JunB (Santa Cruz, sc-73, k0311)


title: Day 3 differentiated H1 derived EMHlin-APLNR+PDGFRa+ cells

growth_protocol: H1 cells were differentiated on OP9 stromal cells for 3 days in a medium containing alpha-MEM/, 10% FBS, 100mM monothioglycerol and 50mg/ml ascorbic acid solutions

value: Anti-human APJ-APC (R&D Systems; cat#FAB856A)

tag: cell type

value: Primitive posterior mesoderm


title: MeDIP_Melanoma_tissue

description: MeDIPed genomic DNA.

source_name: Melanoma tissue, MeDIP

value: primary melanoma

value: empty vector


title: MeDIP_A2058 TET2 M cells

description:
Melanoma cell line A2058 overexpressing full-length catalytically inactive human TET2 mutant.
MeDIPed genomic DNA.

source_name: A2058, TET2 mutant, MeDIP


title: MeDIP_Nevus_tissue

description: MeDIPed genomic DNA.

source_name: Nevus tissue, MeDIP

value: primary benign nevus


title: Th17 BatF

description: Chromatin IP against BATF

value: BATF (from Ken Murphy [rabbit ], not commercial available)


title: BatFKO CD4 T +IL21 IRF4

description: Chromatin IP against IRF4

source_name: CD4+ T Cells


title: Th17 IgG

description: Chromatin IP against IgG

value: Th17 Cells

value: Rabbit IgG (R&D, AB-105-C, ER11)


title: hMeDIP_A2058 TET2 cells

description:
Melanoma cell line A2058 overexpressing full-length wild type human TET2.
hMeDIPed genomic DNA.

data_processing:
Library strategy: hMeDIP
Basecalls performed using CASAVA version 1.8.2.
MeDIP-Seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with unique map and other default parameters to obtain alignments in SAM format.
SAM alignments were converted into BAM format using samtools(v0.1.18(r982:295)).
BAM alignments were converted to BED format using bedtools.
An in-house program was used to remove duplicated reads generated by PCR in the sequencing library, and to extend 300bp based on the strand that is aligned to because the gels for sequencing are cut at about 200-400bp.
Genome_build: hg19
Supplementary_files_format_and_content: BED format.

source_name: A2058, TET2, hMeDIP

value: Active motif


title: hMeDIP_A2058 TET2 M cells

description:
Melanoma cell line A2058 overexpressing full-length catalytically inactive human TET2 mutant.
hMeDIPed genomic DNA.

source_name: A2058, TET2 mutant, hMeDIP


title: hMeDIP_A2058 Mock cells

description:
Melanoma cell line A2058 overexpressing empty vector.
hMeDIPed genomic DNA.

source_name: A2058, mock, hMeDIP


title: Th17 RNASeq

description: 2x polarized

value: Spleen

value: 2x polarized


title: BatFKO CD4 T -IL21 IRF4

description: Chromatin IP against IRF4

value: CD4+ T Cells

value: IRF4 (Santa Cruz, sc-6059, k1209)


title: hMeDIP_Melanoma_tissue

description: hMeDIPed genomic DNA.

source_name: Melanoma tissue, hMeDIP


title: BatFKO CD4 T +IL21 BatF

description: Chromatin IP against BATF


title: hMeDIP_Nevus_tissue

description: hMeDIPed genomic DNA.

source_name: Nevus tissue, hMeDIP


title: IRF4KO CD4 T +IL21 BATF

description: Chromatin IP against BATF


title: Input_A2058 TET2 cells

description:
Melanoma cell line A2058 overexpressing full-length wild type human TET2.
Input sample.

source_name: A2058, TET2, input

value: melanoma cells


title: Input_A2058 TET2 M cells

description:
Melanoma cell line A2058 overexpressing full-length catalytically inactive human TET2 mutant.
Input sample.

source_name: A2058, TET2 mutant, input


title: Input_A2058 Mock cells

description:
Melanoma cell line A2058 overexpressing empty vector.
Input sample.

source_name: A2058, mock, input


title: IRF4KO CD4 T -IL21 BATF

description: Chromatin IP against BATF


title: Input_Melanoma_tissue

description: Input sample.

source_name: Melanoma tissue, input


title: WT CD4 T +IL21 BatF

description: Chromatin IP against BATF


title: Input_Nevus_tissue

description: Input sample.

source_name: Nevus tissue, input


title: WT Bcell IgG

description: Chromatin IP against IgG

source_name: B cells

growth_protocol: For ChIP-Seq, For ChIP-Seq, T and B cells were isolated using kits (Miltenyi). Cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum. For pre-activation, cells were stimulated with plate-bound anti-CD3 (2 ug/ml) + anti-CD28 (1 ug/ml) for 3 days, washed, rested overnight.

extract_protocol: For ChIP-Seq, chromatin was prepared from cells For ChIP-Seq, chromatin was prepared from cells cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication and the ChIP DNA was blunt-ended, ligated to the Solexa adaptor and amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols. and the ChIP DNA was blunt-ended, ligated to the Solexa adaptor and amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols.

value: B cells