title: pol32_OF_sample

city: New York

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

description:
Columns in the bed file are as follows:
column 1: chromosome
column 2: range first bp
column 3: range last bp
column 4: length of fragment in bp
column 5: count of reads
column 6: strand

data_processing: Data were aligned to the May 2008 build of the S. cerevisiae genome: paired-end reads each beginning with a 20bp perfect match to a unique genomic locus and within 1kb of one another were considered.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 30 degrees in YEP + 2% raffinose to O.D. 0.3, then shifted to 37 degrees after addition of galactose to 2% and doxycycline to 40ug/ml

extract_protocol: Genomic DNA was purified and heat-denatured: DNA was bound to Source 15Q resin in batch at 300mM NaCl, pH12, and eluted in 50mM steps. Fractions from 800-900 mM were collected, neutralized and concentrated by precipitation. Double-stranded sequencing adaptors with N6 random overhangs ligated to each end; after second-strand synthesis using Taq, material from 200-1000bp was gel-purified and amplified by PCR. Products from 200-800 bp were gel-purified from two successive 2.5% agarose gels

tag: strain

value: pol32ko [yIW174]

tag: cell cycle stage

value: Asynchronous culture


title: IgG_ChIPSeq

status: Public on Feb 20 2012

type: SRA

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Ctra. de Can Ruti, camí de les escoles, s/n

country: Spain

institute: IMPPC Institut de Medicina Predictiva i Personalitzada del Càncer

library_source: genomic

data_processing: Reads of 36 bp were mapped onto the mouse genome (Mus Musculus reference NCBIM37/mm9, UCSC) using the Bowtie short read aligner (version 0.11.3); a maximum of 2 mismatches, and a 28 bp seed size, were allowed. Only reads mapping to a single position in the genome were used. The CCAT software (v 2.0) was used for peak calling for  the macroH2A reads, with a sliding window size of 1000 bp using the IgG signal as background (available as a Series Supplementary file).

molecule: genomic DNA

organism: Mus musculus

growth_protocol: The mouse ES cell line E14 was maintained in minimal essential medium (MEM, Sigma) supplemented with 20% FBS (Hyclone), 1% penicillin-streptomycin, 1% glutamax, 1% non-essential amino acids, 1% sodium pyruvate, and 0.2% ß-mercaptoethanol, in the presence of leukemia inhibitory factor (LIF) corresponding to 1000 U/ml. The cells were propagated every 2 days by trypsinizing and plating onto 0.1% gelatine-coated plates, with a split ratio of 1:8. Primary human keratinocytes (PHKs), isolated from adult foreskin, were grown on mitomycin C-treated J2-3T3 feeder cells in FAD medium (1 part Ham's F12 medium, 3 parts DMEM, 1.8 X 10^-4 M adenine) supplemented with 10% fetal bovine serum, 0.5 µg/ml hydrocortisone, 5 µg/ml insulin, 10-10 M cholera toxin, and 10 ng/ml EGF. J2-3T3 cells were previously expanded in DMEM containing 10% donor bovine serum and treated with 4 µg/ml mitomycin C (Sigma) for 2 h. For the colony formation assay, 103 PHKs were seeded per well in a 6-well plate on top of a layer of J2-3T3 cells. At the end of the experiment, cells were stained with crystal violet. HEK293T and GP2 cells were cultivated in DMEM supplemented with 10% FCS. For suppression of macroH2A1, cells were infected with vectors expressing either specific or control small hairpin RNAs and selected with 2 mg/ml puromycin.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

treatment_protocol: No treatment Cells were maintained in growth conditions.

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: chip antibody

value: IgG

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #


title: WT_OF_replicate

status: Public on Feb 21 2012

country: USA

value: WT [yIW160]


title: WT_OF_sample


title: pol32_OF_replicate


title: DMC1

city: Bethesda

first: Pavel

middle: P

last: Khil

state: MD

address: 5 Memorial Dr.

institute: NIDDK

description: Standard ChIP-Seq.

data_processing:
DMC1.sorted.ssDNA_type1.bed; genome build: mm9
DMC1.sorted.ssDNA_type2.bed; genome build: mm9
DMC1.sorted.dsDNA.bed; genome build: mm9
DMC1.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.

source_name: adult testis

growth_protocol: Cells were extracted from testis of euthanized mice and subjected to immunoprecipitation.

extract_protocol: Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-RAD51 antibodies. Library construction was done using enzymes from New England Biolabs or Illumina and standard Illumina protocol. Size selection of library fragments of 150~250 bp was performed after PCR amplification. “Klenow exo(-)” sample was prepared by substituting Klenow fragment and T4 DNA polymerase from the end repair step of the standard protocol with Klenow exo(-) enzyme and performing end repair at 37 °C for 1h. “Klenow exo(-), 12 °C“ sample was prepared the same way followed by incubation at 20 °C for 2h and at 12 °C overnight. "Kinetic enrichment" samples were denatured and quickly renatured before adapter ligation.

tag: age

value: adult

tag: gender

value: male

tag: genetic background

value: 9R female x 13R male F1

tag: chip antibody catalog number

tag: chip antibody lot

value: Santa Cruz


title: control 293T RNAseq 4

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: strand-specific RNAseq, hg18

library_source: transcriptomic

data_processing: Strand-specific RNA-seq reads from control siRNA treatment, and each hnRNP depletion experiment were processed as previously described (Polymenidou et al., 2011). An average of 70% of reads mapped uniquely to our gene structure database, using Bowtie (version 0.12.2, with parameters –l 20 –m 5 –k 5 ––best ––un –– max –q).

molecule: polyA RNA

organism: Homo sapiens

source_name: human 293T cells

growth_protocol: Human 293T cells were obtained from ATCC and cultured in DMEM supplemented with 10% FBS at 37 ̊C and 5% CO2.

extract_protocol: Strand-specific RNA-seq libraries were prepared based on the method described in Parkhomchuk et al., 2009, with a few modifications. 10 μg of total RNA was DNase treated (Turbo DNase, Ambion) and then subjected to 2 rounds of polyadenylation selection using Oligo (dT)25 Dynabeads (Invitrogen) according to manufacturer’s recommendations. Eluted mRNA was then reverse transcribed with a mixture of random hexamers and oligo- dT primers. Unincorporated nucleotides were then removed using G-25 spin columns (GE Healthcare) and the second strand of the cDNA was then synthesized in the presence of dUTP instead of dTTP. This reaction was then brought to 350 μl and sonicated on high for 1 hour of 30 seconds on, 30 seconds off sonication bursts. Fragments ranging from 150-225 bp were then selected from a 6% polyacrylamide gel, before the ends of each fragment were repaired using T4 DNA Polymerase, Klenow DNA Polymerase, and T4 PNK (NEB) at 20°C for 1 hour. Enzymes, buffers, and nucleotides in all reactions were removed using Qiagen PCR Purification MinElute columns. Following the end repair, a single dATP was added to each 3′ end using Klenow Exo minus (NEB) at 37°C for 1 hr. The adaptors were then ligated using 2000 units per μl T4 DNA ligase (NEB) at room temperature for 30 minutes. The dUTPs were then removed using Uracil N-Glycosylase (Fermentas) at 37°C for 30 minutes. One half of the library was then subjected to 15 cycles of PCR amplification using Phusion High Fidelity DNA Polymerase (NEB). The library was then separated on a 6% polyacrylamide gel and fragments between 250-325 nucleotides were selected. 8 pM of the resulting amplified libraries were subjected to standard Illumina sequencing protocols.

treatment_protocol: Cells were transfected at 40% confluency using 5μl/ml Lipofectamine-2000 (Invitrogen) and siRNAs at a final concentration of 100nM. For hnRNP A1, A2/B1, H1, M and U, equal mixtures of multiple siRNA sequences were used and for hnRNP F only one siRNA sequence was used. Media was changed 4-6 hrs after the initial transfection, and the transfection was repeated 48 hrs later. Cells intended for RNA analysis were suspended and lysed in TRIzol (Invitrogen) 72 hrs after the first transfection.

tag: treatment

value: Control siRNA

tag: read length


title: MacroH2A_ChIPSeq

description: MacroH2A1 antibody was generated against the aa 128-361 of  mouse macroH2A1 as described in Buschbeck et al. 2009 NSMB.

value: MacroH2A1 (Buschbeck et al, 2009, NSMB)


title: control 293T RNAseq 5

description: strand-specific RNAseq, hg18


title: control 293T RNAseq 6

description: strand-specific RNAseq, hg18


title: hnRNPM 293T RNAseq KD2a

description: strand-specific RNAseq, hg18

value: hnRNPM siRNAs


title: hnRNPM 293T RNAseq KD1b

description: strand-specific RNAseq, hg18


title: hnRNPH1 293T RNAseq KD1a

description: strand-specific RNAseq, hg18

value: hnRNPH1 siRNAs


title: hnRNPM 293T RNAseq KD2b

description: strand-specific RNAseq, hg18


title: control 293T RNAseq 1

description: strand-specific RNAseq, hg18


title: hnRNPU 293T RNAseq KD2a

description: strand-specific RNAseq, hg18

value: hnRNPU siRNAs


title: hnRNPU 293T RNAseq KD1a

description: strand-specific RNAseq, hg18


title: control 293T RNAseq 3

description: strand-specific RNAseq, hg18


title: control 293T RNAseq 2

description: strand-specific RNAseq, hg18


title: hnRNPM 293T RNAseq KD1c

description: strand-specific RNAseq, hg18


title: hnRNPU 293T RNAseq KD2b

description: strand-specific RNAseq, hg18


title: hnRNPH1 293T RNAseq KD2a

description: strand-specific RNAseq, hg18


title: hnRNPF 293T RNAseq KD2c

description: strand-specific RNAseq, hg18

value: hnRNPF siRNA


title: hnRNPM 293T RNAseq KD1a

description: strand-specific RNAseq, hg18


title: hnRNPF 293T RNAseq KD2a

description: strand-specific RNAseq, hg18


title: hnRNPF 293T RNAseq KD1b

description: strand-specific RNAseq, hg18


title: hnRNPF 293T RNAseq KD2b

description: strand-specific RNAseq, hg18


title: hnRNPF 293T RNAseq KD1a

description: strand-specific RNAseq, hg18


title: hnRNPA2B1 293T RNAseq KD2a

description: strand-specific RNAseq, hg18

value: hnRNPA2B1 siRNAs


title: hnRNPA2B1 293T RNAseq KD1a

description: strand-specific RNAseq, hg18


title: hnRNPA1 293T RNAseq KD3d

description: strand-specific RNAseq, hg18

value: hnRNPA1 siRNAs


title: hnRNPA1 293T RNAseq KD3c

description: strand-specific RNAseq, hg18


title: hnRNPU 293T RNAseq KD1b

description: strand-specific RNAseq, hg18


title: hnRNPM 293T RNAseq KD1d

description: strand-specific RNAseq, hg18


title: hnRNPA1 293T RNAseq KD3b

description: strand-specific RNAseq, hg18


title: hnRNPA1 293T RNAseq KD3a

description: strand-specific RNAseq, hg18


title: hnRNPA1 293T RNAseq KD2a

description: strand-specific RNAseq, hg18


title: hnRNPU 293T CLIPseq 4

description: Cross-linking IP against hnRNPU

data_processing: CLIP-seq reads were processed as previously described (Polymenidou et al., 2011). Briefly, reads were trimmed to remove sequencing adaptors and homopolymeric runs >10nt, and mapped to the human genome (hg18) using Bowtie (version 0.12.2 with parameters –q –l 20 –m 5 –k 5 ––best).

molecule: total RNA

extract_protocol: Three 10cm plates of confluent, untreated human 293T cells were subjected to UV cross-linking on ice. CLIP- seq libraries for hnRNP A1, A2/B1, F, M, and U were constructed as previously described (Yeo et al., 2009), using anti-hnRNP A1 (Novus Biologicals), anti-hnRNP A2/B1 (Santa Cruz Biotechnologies), anti-hnRNP F (Santa Cruz Biotechnologies), anti-hnRNP M (Aviva Systems Biology), and anti-hnRNP U (Bethyl Laboratories). Libraries were subjected to standard Illumina sequencing protocols.

tag: antibody

value: hnRNPU

tag: antibody manufacturer

value: Bethyl Laboratories

tag: antibody catalog #

tag: antibody lot #


title: hnRNPU 293T CLIPseq 2

description: Cross-linking IP against hnRNPU


title: hnRNPF 293T CLIPseq 3

description: Cross-linking IP against hnRNPF

value: hnRNPF


title: hnRNPA1 293T CLIPseq 3

description: Cross-linking IP against hnRNPA1

value: Novus Biologicals


title: hnRNPM 293T CLIPseq 1

description: Cross-linking IP against hnRNPM

value: hnRNPM

value: Aviva Systems Biology


title: hnRNPF 293T CLIPseq 4

description: Cross-linking IP against hnRNPF


title: hnRNPF 293T CLIPseq 1

description: Cross-linking IP against hnRNPF


title: hnRNPA1 293T CLIPseq 2

description: Cross-linking IP against hnRNPA1


title: hnRNPA2B1 293T CLIPseq 1

description: Cross-linking IP against hnRNPA2B1


title: hnRNPM 293T CLIPseq 2

description: Cross-linking IP against hnRNPM


title: hnRNPF 293T CLIPseq 2

description: Cross-linking IP against hnRNPF


title: zebrafish Ab zgata1

status: Public on Feb 17 2012

city: Boston

first: Anthony

middle: Dominc

last: DiBiase

state: MA

address: KFRB, 1 Blackfan St, Suite 8216

department: Hem/Onc

institute: Children's Hospital Boston

description:
red blood cells from 10 adults
Chromatin IP against Ab zebrafish gata1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all WICMT samples, reads were aligned to their indicated build using Eland.
For all WICMT samples, aligned sequences were processed with MACS (Zhang et al., 2008) software to produce a single difference signal:  control = WCE, treatment = gata1 ChIP, and with command line input parameters: gsize = 15000000000; bandwidth = 50; and p-value = 1e-09.
For all HMSBPF samples, reads were aligned to their indicated build using SOAP2
For all HMSBPF samples, aligned sequences were processed with MACS (Zhang et al., 2008) software to produce a single difference signal: control = WCE, treatment = H3K4me3, and with command line input parameters: gsize = 15000000000; bandwidth = 50; and p-value = 1e-09.

organism: Danio rerio

source_name: adult red blood cells

growth_protocol: primar red cells isolated from adult zebrafish

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody vendor

value: ANAspec

tag: antibody catalog#

value: adult red blood cells


title: zebrafish adult red cells DnaseI

description: DNaseI in zebrafish adult red blood cells

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using "bowtie -p 8  --mm -n 3 -v 3 -k 2  --phred33-quals". BAM files were created by combining FASTQ files using samtools merge function.
For all samples, aligned sequences were processed with MACS (Zhang et al., 2008) software with command line input parameters: gsize = 15000000000; bandwidth = 50; and p-value = 1e-09.

extract_protocol:
Zebrafish peripheral blood was collected by cardiac puncture in anesthetized adult zebrafish.  As the mature erythrocytes in lower vertebrates retain their nuclei, we are able to isolate erythrocyte nuclei from peripheral blood.  DNase I hypersensitivity assays were arried out.  Briefly, red blood cells were treated with 0.025% Igepal in Buffer A (15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM Spermidine) for 8 minutes.  The released nuclei were pelleted and incubated for 3 minutes at 37C in DNase buffer (13.5mM Tris-Cl pH8.0, 88.5 mM NaCl, 54 mM KCl, 0.9 mM EDTA, 0.45 mM EGTA, 0.45 mM Spermidine, 6 mM CaCl2) plus 0, 40, 60, 80 or120 units/ml of DNaseI (Sigma Aldrich). The reaction was stopped by the addition of an equivalent volume of Stop Buffer (50mM Tris-Cl pH 8.0, 100 mM NaCl, 0.10 %SDS, 100 mM EDTA) and incubated for 1 hr with 1100 units/ml Proteinase K.  Small DNase I fragments from the 120 unit DNaseI treatement were enriched using a sucrose gradient.  These ends were then labeled and amplified for Solexa sequencing
Small genomic DNA fragments resulted from DNase I treatment of intact nuclei were enriched using a sucrose gradient centrifugation after optimal DNase I treatment of isolated nuclei

tag: tissue


title: zebrafish Ab WCE

description: red blood cells from 10 adults

tag: chip antibody

tag: cell type


title: Lin28-RV GFP+ DP thymocytes

first: Cuong

middle: Kieu

last: Nguyen

address: 9000 Rockville Pike

department: NIAID

institute: NIH

data_processing:
DP_Lin28RV_GFP_WT.bedgraph; genome build: mm9
Raw reads were mapped to the mouse genome (NCBI 37, mm9) using the spliced read aligner TopHat version 1.3.1 with option --mate-inner-dist 160 --coverage-search -- microexon-search --max-multihits 20. bamToBed (BedTools v2.11.0, http://code.google.com/p/bedtools/) was used to convert resulting bam files to bed files, then genomeCoverageBed (BedTools v2.11.0, http://code.google.com/p/bedtools/) was used to convert bed files to bedgraph files.

source_name: Lin28-RV GFP+ DP thymocytes

growth_protocol: Retrogenic bone marrow chimeras were generated by transduction of wildtype bone marrow hematopoietic stem and progenitor cells with a retrovirus encoding Lin28a in vitro in the presence of SCF (50 ng/ml), IL-6 (10 ng/ml), IL-3 (5ng/ml), FLT-3L (5ng/ml) and IL- 7 (5ng/ml). A mixture of transduced and untransduced cells were injected into sublethally (450RADS) irradiated Rag1-/- hosts at 2-4 million cells per host.

extract_protocol: RNAseq library preparation was performed starting with 3.3 μg of total RNA using the Truseq RNA sample prep kit (Illumina) following manufacturer’s protocol. Briefly, oligo-dT purified and fragmented mRNA was subjected to first and second strand cDNA synthesis.  cDNA fragments were blunt-ended, ligated to Illumina adaptors, and PCR amplified to enrich for the fragments ligated to adaptors.  The resulting cDNA libraries were verified and quantified on Agilent Bioanalyzer, and sequenced by paired-end RNA-seq using the GAIIx sequencing system (Illumina).

treatment_protocol: Six weeks post-adoptive transfer, RNA was extracted from FACS-sorted GFP+ and GFP- DP thymocytes (CD4+ CD8+ CD3-) and pooled from three retrogenic bone marrow chimeric mice.  RNA concentration was determined using the Qubit RNA broad range assay and fluorometer (Invitrogen).  To confirm the concentration and determine the integrity of the RNA, we used the Eukaryote Total RNA nano Series II chip on a 2100 Bioanalyzer (Agilent).

tag: strain

value: thymocytes

tag: variation

value: CD3- CD4+ CD8+ DP


title: hnRNPU 293T CLIPseq 3

description: Cross-linking IP against hnRNPU

tag: cell line


title: JSL1 resting

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto

description: RNA-Seq performed on polyadenylated RNA

data_processing:
The sequence reads were aligned to human RefSeq sequences using Blat (Kent 2002).
Genome Build:
s_2_tag.txt.fa.filtered.blatRefSeq.resting: human build 36
s_3_tag.txt.fa.filtered.blatRefSeq.resting: human build 36
s_4_tag.txt.fa.filtered.blatRefSeq.resting: human build 36

source_name: JSL1 human T Cell line

growth_protocol: JSL1 cells (Lynch, 2000) were cultured in RPM1 supplemented with 5% heat-inactivated fetal bovine serum (FBS).

extract_protocol: Illumina FastTrack mRNA-Seq library construction

treatment_protocol: For stimulations, JSL1 cells were cultured with PMA (10ng/ml, Sigma), ionomycin (1um, Sigma) or both for 60 hours.

tag: rna subtype

value: polyA+ RNA

tag: activation status

value: resting


title: hnRNPU 293T CLIPseq 1

description: Cross-linking IP against hnRNPU


title: hnRNPA1 293T RNAseq KD1a

description: strand-specific RNAseq, hg18


title: zebrafish adult red cells H3K4me3

description:
red blood cells from 10 adults
Chromatin IP genomic H3K4me3

value: Millipore


title: hnRNPA1 293T CLIPseq 1

description: Cross-linking IP against hnRNPA1


title: Lin28-RV GFP- DP thymocytes

data_processing:
DP_Lin28RV_GFP_KO.bedgraph; genome build: mm9
Raw reads were mapped to the mouse genome (NCBI 37, mm9) using the spliced read aligner TopHat version 1.3.1 with option --mate-inner-dist 160 --coverage-search -- microexon-search --max-multihits 20. bamToBed (BedTools v2.11.0, http://code.google.com/p/bedtools/) was used to convert resulting bam files to bed files, then genomeCoverageBed (BedTools v2.11.0, http://code.google.com/p/bedtools/) was used to convert bed files to bedgraph files.

source_name: Lin28-RV GFP- DP thymocytes


title: JSL1 stimulation with PMA

description: RNA-Seq performed on polyadenylated RNA

data_processing:
The sequence reads were aligned to human RefSeq sequences using Blat (Kent 2002).
Genome Build:
s_2_tag.txt.fa.filtered.blatRefSeq.stimulation: human build 36
s_3_tag.txt.fa.filtered.blatRefSeq.stimulation: human build 36
s_4_tag.txt.fa.filtered.blatRefSeq.stimulation: human build 36

value: stimulation with PMA


title: Blastula (24 hpf)

city: Berlin

first: Jonas

last: Maaskola

address: Robert-Roessle Str. 10

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max-Delbrueck Centrum Berlin-Buch

data_processing: Solexa reads were base called using the manufacturer's software SCS 2.5 / RTA 1.5.

organism: Strongylocentrotus purpuratus

source_name: Strongylocentrotus purpuratus

growth_protocol: Standard conditions

extract_protocol: Total RNA was extracted from the ovary, eggs, 32-cell stage (5 hpf), blastula (24 hpf), gastrula (48 hpf), and pluteus (72 hpf) stages with TriZol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions with the following modifications: samples were initially extracted with chloroform several times until the aqueous phases were free of visible proteins and all RNAs were precipitated overnight at − 20 °C. Small RNA were size selected (18–40 nt) on a 6% Urea-polyacrylamide gel. Sequencing libraries for each sample were prepared with a 5′ monophosphate dependent cloning protocol from Illumina (DGE small RNA; Illumina Inc., CA) and sequenced on the Genome Analyzer 2 (Illumina).

tag: developmental stage

value: Blastula (24 hpf)


title: Gastrula (48 hpf)

value: Gastrula (48 hpf)


title: Pluteus (72 hpf)

value: Pluteus (72 hpf)


title: hnRNPA1 293T CLIPseq 4

description: Cross-linking IP against hnRNPA1


title: zebrafish adult red cells Total Input

description: red blood cells from 10 adults


title: zebrafish adult liver cells DnaseI

description: DNaseI in zebrafish adult liver cells

source_name: adult liver cells

value: adult liver cells


title: 32-cell stage embryo

value: 32-cell stage embryo


title: Egg

value: Egg


title: Ovaries

value: Ovaries


title: Hela_hnRNPU_CLIP_rep2

status: Public on Feb 16 2012

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

description: library from hnRNP U-RNA complex

data_processing:
Hela_hnRNPU_CLIP_rep2.bed; genome build: hg18
Library strategy: CLIP-seq
After removing 3' adaptor sequence, the tags longer than 20 nt were mapped to the reference human genome (hg18) with Bowtie by allowing maximum 2 mismatches in the first 25 nt, and only tags with less than or equal to 10 mapped locations were kept.

source_name: HeLa cells

growth_protocol: HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) with 10% newborn bovine serum plus 100 U penicillin /streptomycin (Gibico) at 37°C in 5% CO2.

extract_protocol: HeLa cells were UV-irradiated at 400 mj and collected by scraping the cells from 15-cm plates. hnRNP U immunoprecipitation was done in 1% NP-40 wash buffer. 3' adaptor was first added to the immunoprecipitated hnRNP U-RNA complex on beads, then the eluted protein-RNA complex was subject to 10% Novex NUPAGE gel. After transfering to NC membrane, the corresponding band was cut and RNA was extracted. After 5' adaptor liagtion, RT-PCR was performed by using Super Script III and Ex taq polymerase.

value: HeLa

value: monoclonal anti-hnRNP U antibody (3G6)


title: Hi-C WT I-SceI-chr15-R1

city: Worcester

first: Rachel

middle: Patton

last: McCord

address: 364 Plantation St. LRB 570M

department: Program in Gene Function and Expression

institute: University of Massachusetts Medical School

description:
416I818-STI2d-R1
The WT cells are from a cell line generated (for this study) from hBcl-2 transgenic mice (Strasser et al., 1991 Cell (PMID 1959134)).

data_processing:
Image analysis pipeline: OLB1.9/CASAVA1.8
For NovoOutput Files: Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters.  If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped.
For Valid Pair files: Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations.  Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR.  Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads.
Genome Build:
s_5_1_WT-416I818-R1.novoOutput.txt.gz: mm9
s_5_2_WT-416I818-R1.novoOutput.txt.gz: mm9
WT-416I818-R1.validPair.txt.gz: mm9

source_name: A-MuLV-transformed pro-B cell line, WT

growth_protocol: A retroviral construct containing 26X I-SceI sites was randomly integrated in the genome of A-MuLV-transformed pro-B cell lines.

extract_protocol: Cells were crosslinked in 1% formaldehyde.  25 million cells were used for each Hi-C experiment.  Cells were lysed and chromatin was digested with HindIII as described previously (Lieberman-Aiden et al., 2009 (PMID 19815776)).  Digested ends were filled in with biotinylated dCTP and then ligated for 4 hours at 16 C.  After reversing the formaldehyde crosslinks by incubation at 65 C with Proteinase K overnight, unligated biotinylated ends were removed by 4 hours of incubation with 15 U T4 DNA polymerase at 20 C in the presence of a low concentration of nucleotides (25 µM each dNTP).  The DNA was fragmented by Covaris sonication to an average size of 200 bp and then the ideal size for Illumina sequencing (100-300 bp) was selected by Ampure fractionation (0.9x Ampure beads to remove the DNA fragments >300 bp followed by 1.3x Ampure beads to isolate the remaining DNA fragments > 100 bp).  The DNA ends were prepared for Illumina sequencing adapter ligation by repairing the DNA ends and adding an 'A'  to each end.  The biotinylated junctions were then pulled down using MyOne streptavidin beads at a ratio of 1 uL beads per ng of biotinylated DNA.  Illumina paired-end adapters were ligated onto the DNA ends and then the fragments were PCR amplified for 11-13 cycles.  Samples were sequenced on an Illumina HiSeq instrument using the Paired End 50 bp module.

treatment_protocol: Cells were arrested in G1 by 2 days of treatment with 3µM STI571.

value: A-MuLV transformed pro-B cells

tag: genotype

value: WT

tag: treatment

value: STI571 for 2d

tag: i-scei integration location (mm9)

tag: biological replicate


title: Hi-C WT I-SceI-chr2-R1

description:
416I825-STI2d-R1
The WT cells are from a cell line generated (for this study) from hBcl-2 transgenic mice (Strasser et al., 1991 Cell (PMID 1959134)).

data_processing:
Image analysis pipeline: OLB1.9/CASAVA1.8
For NovoOutput Files: Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters.  If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped.
For Valid Pair files: Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations.  Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR.  Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads.
Genome Build:
s_4_1_WT-416I825-R1.novoOutput.txt.gz: mm9
s_4_2_WT-416I825-R1.novoOutput.txt.gz: mm9
WT-416I825-R1.validPair.txt.gz: mm9


title: Snyder_FOS-1_Input_L1_rep1 extraction1_seq1 aliquote 1

first: DCC

last: modENCODE

state: Ontario

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

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 WS180

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.

value: OP304(official name :OP304 genotype :unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119) 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 FOS-1::EGFP fusion protein is expressed in the correct fos-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FOS-1 transcription factor. made_by :R Waterston )

value: fed L1

tag: Sex

value: Hermaphrodite


title: Hi-C ATM-/- I-SceI-chr7-R1

description:
5353-STI2d-R1
The ATM2E-I13 cell line is derived (stably transfected with I-SceI-GR) from the ATM2E cell line (Bredemeyer et al., 2006, Nature (PMID 16799570)), which was generated from an ATM-/- mouse (Barlow et al., 1996, Cell (PMID 8689683)) with an hBcl-2 transgene (Strasser et al., 1991 Cell (PMID 1959134)).

data_processing:
Image analysis pipeline: OLB1.9/CASAVA 1.7
For NovoOutput Files: Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters.  If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped.
For Valid Pair files: Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations.  Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR.  Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads.
Genome Build:
s_4_1_ATM-5353-R1.novoOutput.txt.gz: mm9
s_4_2_ATM-5353-R1.novoOutput.txt.gz: mm9
ATM-5353-R1.validPair.txt.gz: mm9

source_name: A-MuLV-transformed pro-B cell line, ATM-/-

value: ATM-/-


title: Snyder_FOS-1_Input_L1_rep2 extraction1_seq1 aliquote 1

description: input DNA


title: Hi-C ATM-/- I-SceI-chr18-R2

description:
5714-STI2d-R2
The ATM2E-I13 cell line is derived (stably transfected with I-SceI-GR) from the ATM2E cell line (Bredemeyer et al., 2006, Nature (PMID 16799570)), which was generated from an ATM-/- mouse (Barlow et al., 1996, Cell (PMID 8689683)) with an hBcl-2 transgene (Strasser et al., 1991 Cell (PMID 1959134)).

data_processing:
Image analysis pipeline: OLB1.9/CASAVA 1.7
For NovoOutput Files: Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters.  If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped.
For Valid Pair files: Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations.  Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR.  Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads.
Genome Build:
s_7_1_ATM-5714-R2.novoOutput.txt.gz: mm9
s_7_2_ATM-5714-R2.novoOutput.txt.gz: mm9
ATM-5714-R2.validPair.txt.gz: mm9


title: Hi-C ATM-/- I-SceI-chr2-R1

description:
67-STI2d-R1
The ATM2E-I13 cell line is derived (stably transfected with I-SceI-GR) from the ATM2E cell line (Bredemeyer et al., 2006, Nature (PMID 16799570)), which was generated from an ATM-/- mouse (Barlow et al., 1996, Cell (PMID 8689683)) with an hBcl-2 transgene (Strasser et al., 1991 Cell (PMID 1959134)).

data_processing:
Image analysis pipeline: OLB1.9/CASAVA 1.7
For NovoOutput Files: Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters.  If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped.
For Valid Pair files: Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations.  Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR.  Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads.
Genome Build:
s_6_1_ATM-67-R1.novoOutput.txt.gz: mm9
s_6_2_ATM-67-R1.novoOutput.txt.gz: mm9
ATM-67-R1.validPair.txt.gz: mm9


title: Snyder_FOS-1_GFP_L1_rep1 extraction1_seq1 aliquote 1

description: ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;input DNA


title: Snyder_FOS-1_GFP_L1_rep2 extraction1_seq1 aliquote 1


title: Hela_hnRNPU_RNAseq_control

description: Control cells

data_processing:
Hela_hnRNPU_RNAseq_control.bed; genome build: hg18
Paired-end reads were separately mapped into a custom Bowtie index, which was built from UCSC knownGenes (hg18) not including introns. Under the constraint of the insert size, only the paired-end reads whose two ends are about 50 nt apart on the same gene were kept. For each pair, the coordinates of the two end reads were mapped back to the genome based on its gene's genomic location, and then joined together. Only the pair-end reads with one unique genomic location were kept.

extract_protocol: Total RNAs were extracted by Trizol from treated HeLa cells and polyA RNAs were enriched by oligod(T) selection. After fragmentation, mRNAs were reversely transcribed to cDNA with Superscript II in the presence of random primer. After RNase H digestion, the second strand cDNA was synthesized by DNA pol I followed by adaptor ligation. Size-selected PCR products were sequenced by Illumila Genome Analyzer II.

treatment_protocol: Transfection of control siRNA

tag: transfection

value: Control


title: Hi-C ATM-/- I-SceI-chr2-R2

description:
67-STI2d-R2
The ATM2E-I13 cell line is derived (stably transfected with I-SceI-GR) from the ATM2E cell line (Bredemeyer et al., 2006, Nature (PMID 16799570)), which was generated from an ATM-/- mouse (Barlow et al., 1996, Cell (PMID 8689683)) with an hBcl-2 transgene (Strasser et al., 1991 Cell (PMID 1959134)).

data_processing:
Image analysis pipeline: OLB1.9/CASAVA 1.7
For NovoOutput Files: Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters.  If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped.
For Valid Pair files: Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations.  Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR.  Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads.
Genome Build:
s_5_1_ATM-67-R2.novoOutput.txt.gz: mm9
s_5_2_ATM-67-R2.novoOutput.txt.gz: mm9
ATM-67-R2.validPair.txt.gz: mm9


title: Hi-C ATM-/- I-SceI-chr18-R1

description:
5714-STI2d-R1
The ATM2E-I13 cell line is derived (stably transfected with I-SceI-GR) from the ATM2E cell line (Bredemeyer et al., 2006, Nature (PMID 16799570)), which was generated from an ATM-/- mouse (Barlow et al., 1996, Cell (PMID 8689683)) with an hBcl-2 transgene (Strasser et al., 1991 Cell (PMID 1959134)).

data_processing:
Image analysis pipeline: OLB1.9/CASAVA 1.7
For NovoOutput Files: Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters.  If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped.
For Valid Pair files: Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations.  Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR.  Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads.
Genome Build:
s_1_1_ATM-5714-R1.novoOutput.txt.gz: mm9
s_1_2_ATM-5714-R1.novoOutput.txt.gz: mm9
ATM-5714-R1.validPair.txt.gz: mm9


title: gHD_unmatched_sites

status: Public on Feb 15 2012

first: Scot

last: Wolfe

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

description:
sequences that did not match any barcodes for specificity selected against the ZF10 library for the grafted homeodomians (samples 220-243)
molecule: plasmid DNA

library_source: other

data_processing: Processed data not applicable for this record.

molecule: other

organism: synthetic construct

source_name: synthetic library

growth_protocol: For each selection using the HD library at least 1x108 dual transformants (of HD expression vector and binding site reporter vector into the selection strain) were plated on NM media supplemented with 1uM IPTG and 200uM uracil.  The stringency of each selection was adjusted such that 1000-2000 colonies were recovered.  For each selection using the ZF10 libaray selections was performed that all selections were plated on NM media supplemented with 5mM 3-AT, 1uM IPTG, and 200uM uracil.

extract_protocol: For HD library-- Surviving colonies from each selection were pooled and prepared for sequencing).  HD clones were amplified using a forward primer (CAAGCAGAAGACGGCATACGAGCTCTTCCGATCTATGCTTGCCCTGTCGAGTCC) and reverse primer (CTTAATGCGCCGCTACAGGGC), where the forward primer incorporated the Illumina P2-adapter sequence.  Each PCR product was then digested with either BamHI or XbaI for the ligation of barcoded P1 adapters  prior to Illumina library generation and sequencing.  Recovered ZF10 library members were identified via Illumina sequencing, the initial PCR product was digested with either BamHI or NcoI for the ligation of barcoded P1 adaptors (Table S1 & S5).

tag: library selection

value: bacterial one-hybrid (B1H) selected


title: RH_unmatched_sites

description:
sequences that did not match any barcodes for homeodamains selected against the triplet site selections (samples 1-64)
molecule: plasmid DNA


title: x1st_unmatched_sites

description:
sequences that did not match any barcodes for the 1st round (samples 65-139) of homeodomain selections for specificity
molecule: plasmid DNA


title: ntermHD_unmatched_sites

description:
sequences that did not match any barcodes for the N-terminal arm (samples 244-346) of homeodomain selections for specificity
molecule: plasmid DNA


title: rat siSupt4h

city: Stanford

first: Ning

last: Deng

address: 300 Pasteur Drive, RmL-314

department: Genetics Department

institute: Stanford University

description:
RNA-seq
insert size is 150bp-350 bp

library_source: non-genomic

data_processing: Raw data were uploaded to https://dnanexus.com and RNA-Seq/Transcriptome-base quantification analyses were performed to the samples.

organism: Rattus norvegicus

source_name: striatal neural cells

extract_protocol: mRNA was purified by Dynabeads® mRNA Purification Kit from total RNA. Then they were fragmented and reverse-transcribed as double strand cDNA by Super-script double-stranded cDNA synthesis kit from Invitrogen (Cat. 11917-010). The DNA then was end-repaired. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 150bp-350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequencedfollowing the manufacturer's protocols.

treatment_protocol: mammalian cells were transfected with NC siRNA or siSupt4h

value: striatal neural cells


title: rat siCtr

description:
RNA-seq
insert size is 150bp-350 bp


title: Hela_hnRNPU_CLIP_rep1

description: library from hnRNP U-RNA complex

data_processing:
Hela_hnRNPU_CLIP_rep1.bed; genome build: hg18
Library strategy: CLIP-seq
After removing 3' adaptor sequence, the tags longer than 20 nt were mapped to the reference human genome (hg18) with Bowtie by allowing maximum 2 mismatches in the first 25 nt, and only tags with less than or equal to 10 mapped locations were kept.

tag: antibody


title: Yeast Spt4 Del-2

description:
RNA-seq
insert size is 150bp-350 bp

source_name: yeast

value: yeast

tag: genetic background


title: Yeast Spt4 Del-1

description:
RNA-seq
insert size is 150bp-350 bp


title: Narm216_NRVMM

description:
selected from the bacterial-one hybrid system
molecule: plasmid DNA

data_processing: Each fasta line represents a unique sequence identified where the HD interacts with that DNA sequence.

source_name: synthetic library--Z10 library

tag: library

value: Z10 library


title: 3rd_unmatched_sites

description:
sequences that did not match any barcodes for the 3rd round (300's, samples308-318) of homeodomain selections for specificity
molecule: plasmid DNA


title: Narm219_KVYER


title: Narm40_STRER


title: Yeast WT-2

description:
RNA-seq
insert size is 150bp-350 bp

tag: cell type


title: Yeast WT-1

description:
RNA-seq
insert size is 150bp-350 bp


title: 24_Ubx_WT


title: Hela_hnRNPU_RNAseq_knockdown

description: hnRNP U knockdown cells

data_processing:
Hela_hnRNPU_RNAseq_knockdown.bed; genome build: hg18
Paired-end reads were separately mapped into a custom Bowtie index, which was built from UCSC knownGenes (hg18) not including introns. Under the constraint of the insert size, only the paired-end reads whose two ends are about 50 nt apart on the same gene were kept. For each pair, the coordinates of the two end reads were mapped back to the genome based on its gene's genomic location, and then joined together. Only the pair-end reads with one unique genomic location were kept.

treatment_protocol: Transfection of siRNA against hnRNP U

value: hnRNP U knockdown


title: 23_Ubx_LAKDQ


title: 22_Ubx_RSNQK


title: 21_Ubx_TQRQW


title: 19_Ubx_ERVSR


title: 20_Ubx_TRMAF


title: 16_Scr_WT


title: 14_Scr_RSNQK


title: 12_Scr_TRMAF


title: 13_Scr_TQRQW


title: 15_Scr_LAKDQ


title: 11_Scr_ERVSR


title: 8_Dfd_WT


title: 10_Scr_HLIQY


title: 9_Scr_ATVKA


title: 7_Dfd_LAKDQ


title: 6_Dfd_RSNQK


title: 4_Dfd_TRMAF


title: 2_Dfd_HLIQY


title: 3_Dfd_ERVSR


title: 311_GTC_YRRGF


title: 5_Dfd_TQRQW


title: 1_Dfd_ATVKA


title: 306_GCA_RHDRA


title: 308_GCG_RLDRF


title: 309_GCG_RLDRY


title: 310_GTC_YRRGA


title: 17_Ubx_ATVKA


title: 18_Ubx_HLIQY


title: 305_GAT_VGRLY


title: 303_CTC_VMNRK


title: 302_ATA_LRWNS


title: 304_CTG_TTNQK


title: 270_AAG_RAQWF


title: 266_ACC_KACHS


title: 267_ACA_RVSHT


title: 307_GCA_RYDRA


title: 301_AAG_RSQWH


title: 272_AAC_VAQRC


title: 269_AAT_KVTNF


title: 271_AAC_KLQRF


title: 265_ACG_WYSKY


title: 261_AGG_KSKEA


title: 262_AGA_QFRAW


title: 263_AGA_VRFAA


title: 260_ATA_KAYNA


title: 259_ATA_KMYAW


title: 264_ACT_KVYHV


title: 258_ATT_RTVQQ


title: 268_AAT_KLQAF


title: 256_CCA_RLYQK


title: 247_GCG_RTDRS


title: 250_GAT_AGKTF


title: 251_CTT_VGYSR


title: 246_GCT_ISVKY


title: 253_CGT_VANSR


title: 257_CAT_KLCSR


title: 242_GTC_LQRGA


title: 244_GGT_KMKSV


title: 243_GGT_ATKSM


title: 245_GCT_RAVKW


title: 241_GTT_GLRAF


title: 249_GCA_QLKQS


title: 252_CTC_LRYSK


title: 240_GTT_SSRGF


title: 255_CCT_RADGK


title: 239_TAA_RTVRA


title: 235_TAT_RAVSV


title: 238_TAC_QRISV


title: 236_TAG_KSTQM


title: 237_TAG_YAVNA


title: 233_TCG_VMNQQ


title: 234_TCA_AMVQR


title: 232_TCG_IKNQM


title: 228_TTG_KMLQA


title: 229_TTC_GRISA


title: 227_TTT_YRIAA


title: 226_TTT_KMISA


title: 230_TGC_ERISQ


title: 225_AAC_SLQRF


title: 224_CCC_IMNSK


title: 223_CTC_RTFGK


title: 221_CTG_RLYQK


title: 219_CTG_KVYER


title: 222_CTC_SKYGK


title: 217_GGG_KSKEG


title: 220_CTG_LTYQK


title: 215_TTC_KRLAA


title: 213_AGG_KMKES


title: 212_ATA_RVTNA


title: 210_CCG_RSNQK


title: 211_ATT_TKNQN


title: 208_CTC_HFNRK


title: 209_CGC_PRDSR


title: 207_CTT_ITYGK


title: 204_GCG_RTDRY


title: 203_GTC_VQKRF


title: 201_TGC_VRVSQ


title: 205_GAA_TQRQW


title: 168_ACG_SRYDR


title: 202_GTG_NAREF


title: 77_AAA_KEYVH


title: 72_AAT_KMSNF


title: 218_CTG_KQNQK


title: 76_AAA_RAQWF


title: 216_TGC_NRVMM


title: 65_AGA_GSRWY


title: 70_ACC_KTSHM


title: 66_ACT_KTSHM


title: 67_ACT_MKYEK


title: 69_ACG_VKYER


title: 63_AGC_QSRNV


title: 60_ATA_KTVQV


title: 61_AGT_KGKEW


title: 54_CAA_LMYQR


title: 58_ATG_RVYQW


title: 55_CAA_LHYVR


title: 57_ATG_LTYQW


title: 51_CAG_MSHWR


title: 53_CAC_ERVSR


title: 52_CAC_LGMRR


title: 59_ATC_TRMAF


title: 73_AAT_KLTAF


title: 49_CAT_LSQSR


title: 71_ACA_MTNNR


title: 75_AAC_SISRF


title: 48_CCA_EHNAK


title: 50_CAT_MMCSR


title: 47_CCA_KMTQK


title: 44_CCT_RGDSK


title: 74_AAG_STSAH


title: 46_CCC_RLDSK


title: 62_AGG_SHKEY


title: 64_AGA_AFRAH


title: 42_CGA_TFYAA


title: 43_CCT_MTNGK


title: 39_CTA_IFNAK


title: 41_CGC_RVMSR


title: 56_ATT_HRVQA


title: 38_CTA_LHYAK


title: 37_GAA_RFQKF


title: 36_GAC_ATRRF


title: 32_GCC_VRLKY


title: 33_GCA_ALRQQ


title: 30_GGA_LAKDQ


title: 29_GGC_TLKNQ


title: 28_GGG_RSKER


title: 35_GAG_VMRWY


title: 34_GAT_RTMRY


title: 27_GGT_LTKDQ


title: 45_CCG_RCYEK


title: 24_GTG_HLIQY


title: 26_GGT_ALKNM


title: 23_GTT_GTRAY


title: 25_GTA_YTRQV


title: 40_CGG_STRER


title: 21_TAC_ERVSV


title: 22_TAA_RITAA


title: 19_TAG_RMVSA


title: 17_TAT_TRVSA


title: 18_TAG_RLTQA


title: 20_TAC_QRVSA


title: 15_TCC_RMIKS


title: 12_TGA_RGVAA


title: 14_TCG_KGTQM


title: 13_TCT_ATVKA


title: 7_TTA_RVLRA


title: 8_TGT_RVVSQ


title: 10_TGG_KSVMQ


title: 9_TGG_KTTQD


title: 31_GCT_KITKF


title: 5_TTC_TRVAA


title: 6_TTA_VRVAA


title: 4_TTC_VRVSA


title: tripletAAA

source_name: synthetic library--HD library

value: HD library


title: 2_TTT_RTVSA


title: 1_TTT_RTVAA


title: tripletAAC


title: tripletAAT


title: tripletACG


title: tripletACC


title: tripletACT


title: tripletAAG


title: tripletAGA


title: tripletACA


title: 11_TGA_KSVAQ


title: tripletAGG


title: tripletATC


title: tripletATA


title: tripletAGT


title: tripletATG


title: tripletATT


title: tripletCAA


title: tripletCAG


title: tripletCAC


title: tripletCCC


title: tripletCCG


title: tripletCCT


title: tripletCGA


title: tripletCGC


title: tripletCGG


title: tripletCTC


title: tripletAGC


title: tripletCGT


title: tripletCTG


title: tripletGAC


title: tripletCTT


title: tripletGCA


title: tripletGAT


title: tripletGAG


title: tripletGCG


title: tripletGCC


title: tripletGGA


title: tripletGGT


title: tripletGGG


title: tripletCAT


title: tripletGTG


title: tripletCCA


title: tripletGTC


title: tripletGTA


title: tripletGGC


title: tripletTAG


title: tripletGTT


title: tripletTAA


title: tripletTAC


title: tripletTAT


title: tripletTCA


title: tripletCTA


title: tripletTCC


title: tripletGAA


title: tripletTCG


title: tripletTGC


title: tripletTCT


title: tripletGCT


title: tripletTGA


title: tripletTTT


title: tripletTTC


title: tripletTTA


title: tripletTGT


title: tripletTGG


title: tripletTTG


title: mouse siSupt4h

description:
RNA-seq
insert size is 150bp-350 bp


title: F1i_BstNI_Seq

city: San Diego

first: Wei

last: Xie

address: 9500 Gilman Dr. CMM East, Room 2071

data_processing: FspEI-Seq reads were mapped using Novoalign (Novocraft, Malaysia) with adapter sequences stripped. Novoalign permits gapped alignment by allowing more than two mismatches per read (up to 8 for high quality base calls on single end reads and 16 on paired-end reads) that particularly benefits sequencing read mapping around SNPs and indels. Only reads that were perfectly mapped were used to determine the positions of methylcytosines on the same strand.

source_name: Frontal cortex

growth_protocol: The crosses of the two mouse strains 129x1/SvJ (129) and Cast/EiJ (Cast) were performed at Jackson Laboratories (http://jaxmice.jax.org/) and the male mice F1 offspring and males of each of the two parental strains were shipped to investigator laboratories at 8 to 9 weeks of age.

extract_protocol: A total of 500ng genomic DNA isolated from IMR90, MEF, and the frontal cortex of F1i and F1r was digested in parallel by the DNA methylation dependent restriction enzyme FspEI. FspEI recognizes the CmC site (the second cytosine is methylated and can be in the context of CG, CHG or CHH) and creates a 5’ protruding end 17 bases downstream of the methylcytosine. A similar experiment was performed by incubating the F1i genomic DNA with a DNA methylation independent restriction enzyme BstNI. The digested DNA was gel purified, size selected for fragments within 100-600bp. The resulting DNA was then prepared as genomic DNA libraries for high-throughput sequencing (Illumina).

tag: strain

value: 129X1/SvJ x Cast/EiJ

tag: gender

value: male

tag: tissue

value: frontal cortex


title: mouse siCtr

description:
RNA-seq
insert size is 150bp-350 bp


title: MEF_FspEI_Seq

source_name: MEF cell

tag: sample type

value: murine embryonic fibroblast


title: IMR90_FspEI_Seq

source_name: IMR90 cell

value: human fibroblast IMR90


title: F1r_FspEI_Seq

value: Cast/EiJ x 129X1/SvJ


title: Cast_MethylC_Seq

data_processing: MethylC-Seq reads were mapped using Novoalign (Novocraft, Malaysia) with adapter sequences stripped. Novoalign permits gapped alignment by allowing more than two mismatches per read (up to 8 for high quality base calls on single end reads and 16 on paired-end reads) that particularly benefits sequencing read mapping around SNPs and indels. PCR duplicates for each library were removed with the Picard program(Picard 2011).

extract_protocol: Five µg of genomic DNA was extracted from the frontal cortex of the F1 crosses and was spiked in with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented by sonication to 100-600 bp. Purified DNA fragments were end-repaired and ligated to paired-end cytosine- methylated adapters provided by Illumina. Size-selected adapter-ligated DNA was treated with sodium bisulfite using the EZ DNA methylation-Gold Kit (Zymo Research). The resulting DNA molecules were enriched by PCR, purified and sequenced following standard protocols from Illumina. The average insert sizes of the paired-end libraries are 140bp and 143bp, with the standard deviation of 47bp and 49bp, for the F1i and F1r strains, respectively.

value: Cast/EiJ


title: F1i_FspEI_Seq


title: F1r_MethylC_Seq


title: F1i_RNA_Seq

data_processing: Sequencing reads for the RNA-Seq reads were mapped using Novoalign (Novocraft, Malaysia) . Novoalign permits gapped alignment by allowing more than two mismatches per read (up to 8 for high quality base calls on single end reads and 16 on paired-end reads)

extract_protocol: The frontal cortex from the F1 crosses of the two mouse lines was dissected and the RNA was isolated followed by two DNAseI treatments to remove DNA contaminant.  The presence of DNA in the RNA was tested using quantitative PCR and probes designed to span exons.  The quality of the RNA was determined by the Agilent 2100 Bioanalyzer prior to the construction of the libraries.  RNA was treated with RiboMinus (Invitrogen, Carlsbad CA) to remove the ribosomal RNA.  The methods for the preparation of the libraries are outlined in the Whole Transcriptome library preparation for SOLiD sequencing protocol (https://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_065852.pdf).  Briefly, RNA depleted of ribosomal RNA was fragmented using RNAseIII.  Purified RNA was hybridized and ligated to primers then converted to cDNA using reverse transcriptase.  The cDNA was size selected to contain 50 to 150 bp inserts then purified and amplified prior to sequencing. Libraries were constructed with RNA from three independent mice (3 biological replicates) for each of the experimental crosses. Sequencing was performed at EdgeBio (http://www.edgebio.com/) and the data from the 3 mice for each experimental cross line were combined given the high correlation between each of the libraries (R >0.98).


title: F1i_MethylC_Seq


title: F1r_ChIP_Seq_H3K4me3 (GAII)

data_processing: Sequencing reads for the ChIP-Seq reads were mapped using Novoalign (Novocraft, Malaysia) with adapter sequences stripped. Novoalign permits gapped alignment by allowing more than two mismatches per read (up to 8 for high quality base calls on single end reads and 16 on paired-end reads) that particularly benefits sequencing read mapping around SNPs and indels. PCR duplicates for each library were removed with the Picard program(Picard 2011).

extract_protocol: Frozen mouse frontal cortex from the F1 crosses was thawed on ice and processed with a razor blade into small pieces. Tissue was then crosslinked with formaldehyde, washed, homogenized, and proceeded for ChIP. To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Branson 450 Sonifier (Branson, Danbury, CT). ChIP DNA was subjected to end repair, A-tailing, adaptor ligation, and gel purification. Following PCR amplification for 18 cycles, the final libraries were subjected to sequencing.

tag: chip-antibody

tag: vendor

value: Millipore, 04-745


title: F1i_ChIP_Seq_H3K27ac (GAII)

value: Active Motif, AM39133


title: F1i_ChIP_Seq_input


title: F1i_ChIP_Seq_H3K4me3 (GAII)


title: wild-type_mycelium_GMM

status: Public on Feb 13 2012

city: Exeter

first: Darren

middle: Mark

last: Soanes

address: RILD Building, RD&E Hospital Wonford, Barrack Road

department: College of Medicine and Health

country: United Kingdom

institute: University of Exeter

data_processing: Tophat (http://tophat.cbcb.umd.edu/) was used to align short reads to the published genome (version 6) of Magnaporthe oryzae (http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/MultiHome.html) and to predict exon splice sites. Cufflinks (http://cufflinks.cbcb.umd.edu/) was used to analyse this data (only reads with a mapping quality > 30) using gene annotations from M. oryzae, resulting in normalised counts (expressed in fragments per kilobase of exon model per million mapped fragments - FPKM) for each gene.

organism: Pyricularia oryzae

source_name: mycelium

growth_protocol: Plugs of Guy11 mycelium grown on complete medium (CM) plates were used to innoculate liquid CM medium and were grown in shaking culture for 36 h at 25C, 200rpm. Mycelia were harvested by filtering through 3 layers of miracloth, washed 2-3 times with sterile distilled water (SDW) and blotted dry, before freezing in liquid nitrogen.  Glucose minimal medium (GMM) samples were intially grown in CM as described above, but then transferred to GMM for 16 hours in shaking culture before being harvested.

extract_protocol: Sequencing libraries were prepared using mRNA-Seq Sample Preparation kit from Illumina according to manufacturer's instructions

tag: medium

value: glucose minimal

value: mycelium


title: wild-type_mycelium_GMM_rep3

data_processing: FASTX Barcode Splitter from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/download.html) was used to separate the samples from the same lane using the four base barcode.  FASTA/Q trimmer from the FASTX-Toolkit was used to remove the 4 base barcode from the sequence and then to remove the sequence from position 27 to the end of the sequence leaving a 26 base tag sequence. Any remaining adapter sequences were removed using FASTA/Q clipper from the FASTX-Toolkit. FASTQ-to-FASTA from the FASTX-toolkit was used to convert the tag sequences to a FASTA format. Bespoke perl scripts were used to calculate the frequency of each unique tag in each sample.

extract_protocol: High throughput (HT)-SuperSAGE libraries were prepared as described in Matsumura et al 2010, PLoS One. 5: e12010. Four samples were multiplexed on each lane of the Illumina flow-cell

tag: medium type


title: F1r_RNA_Seq


title: wild-type_mycelium_GMM_rep1


title: wild-type_mycelium_GMM_rep2


title: F1r_ChIP_Seq_input


title: wild-type_mycelium_CM_rep3

value: complete


title: wild-type_mycelium_CM_rep2


title: wild-type_mycelium_CM_rep1


title: 129_MethylC_Seq


title: wild-type_mycelium_CM


title: wild-type germinating conidia 14hrs rep1

source_name: germinating conidia

growth_protocol: Conidia were harvested by flooding 14 day old complete medium-agar plates with sterile distilled water (SDW) and scraping the surface with a glass spreader. Mycelial fragments were removed by filtering though 2-3 layers of Miracloth and conidia were washed three-times with SDW. Conidia were suspended in SDW to a final concentration of 750000 conidia/ml. 1,16-hexadecanediol was added to the suspension to a final concentration of 50 ng/microlitre. For germination, conidia were placed on plastic cover-slips and samples collected at specified times.

tag: genotype

value: wild type

tag: developmental stage

value: germinating conidia

tag: time

value: 14 hrs


title: pmk1 mutant germinating conidia 4hrs rep2

value: pmk1 knockout

value: 4 hrs


title: wild-type germinating conidia 16hrs rep2

value: 16 hrs


title: wild-type germinating conidia 8hrs rep2

value: 8 hrs


title: wild-type germinating conidia 14hrs rep2


title: pmk1 mutant germinating conidia 4hrs rep1


title: F1r_ChIP_Seq_H3K27ac (GAII)


title: wild-type germinating conidia 16hrs rep1


title: wild-type germinating conidia 4hrs rep2


title: Retinal_microvascular_endothelial_cells

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: QUB Institue of clinical Science, Block A, RVH

department: Centre for Experimental Medicine

institute: Queen's University Belfast

data_processing: Adapter sequences were clipped from the raw sequences using Genomics workbench software (CLCbio, Aarhus, Denmark) and a list of unique sequences with the number of reads for each generated

organism: Bos taurus

source_name: Retinal microvasculature

growth_protocol: Retinal microvascular endothelial cells (RMECs) were isolated from bovine retina by established protocols. Briefly, bovine eyes were transported from a local abattoir on ice and the retinas removed and washed free of RPE in Dulbecco's minimal essential medium (DMEM; Life Technologies). The retina was cut into segments, homogenized in MEM and then filtered through an 85 µm filter. The trapped microvessels were digested at 37 °C for approximately 30 min in PBS containing 250 µg/ml pronase, 200 µg/ml DNAase, and 50 µg/ml collagenase. The filtrate was microscopically examined to determine the end point for maximum retrieval of endothelial cells. Vessel fragments were then trapped in a 53 µm filter which was centrifuged at 1100 rpm for 10 minutes.  The pellet was resuspended in Dulbecco's modified Eagles medium (DMEM) containing antibiotic (0.1mg/ml Primocin), 0.38 µg/ml insulin, 1mg/ml heparin and 20% porcine serum (Sigma).  This mixture was seeded into 25 cm2 gelatin-coated Falcon flasks and maintained at 37 °C in a mixture of 5% CO2 and air.  10% porcine serum was used in the culture medium from passage 1 onwards and cells were analysed at passage 2.

extract_protocol: RNA was extracted using a microRNeasy kit (Qiagen). A small RNA library was prepared using a sample prep kit v1.5 kit (Illumina) following the manufacturer's protocol. Briefly, following linker ligation and PCR amplification the range of products corresponding to small RNAs were excised from a 6% polyacrylamide gel

value: Primary retinal endothelial cells

tag: passage


title: wild-type germinating conidia 4hrs rep1


title: PEC_IL10-treated_Input_ChIPseq

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

description: library insert size: 174

data_processing: Alignment: Sequence reads were aligned to the mm9 mouse genome assembly using bowtie. The first two base pairs were discarded, up to 2 mismatches were allowed and reads that aligned to more than one location in the genome were discarded

source_name: Input chromatin from IL-10 treated (4 hours) macrophages

growth_protocol: peritoneal exudate cells were washed from the mouse peritoneum 3 days after (.i.p.) thioglycolate injection. Cells were allowed to adhere for 24 hours and non-adherent cells were washed away with several washes of fresh medium. PEC macrophages where treated with IL-10 (100 ng/ml) for 4 hours.

extract_protocol: Library and Sequencing were performed at BGI, China, using standard Illumnina kits and protocols.

treatment_protocol: peritoneal exudate cell macrophages were treated with 100 ng/ml of IL-10 for four hours. Cells were then harvested by scraping and prepared for ChIP

value: Male

value: Adherent peritoneal exudate macrophages

tag: chip antibody


title: PEC_Untreated_Input_ChIPseq

description: library insert size: 182

source_name: Input chromatin from untreated macrophages


title: PEC_Untreated_STAT3_ChIPseq

description: library insert size: 172

source_name: ChIP in untreated macrophages against STAT3

value: anti-STAT3 (Santa Cruz sc-482)


title: RNA-seq of Untreated macrophages

description:
library insert size: 197
RNA-seq of Untreated treated macrophages

data_processing:
Alignment: Sequence reads were aligned to the mm9 mouse genome assembly using the TopHat and Cufflinks combination
Splice Junctions: A bed file containing the splice junctions as determined by the TopHat and Cufflinks combination

source_name: RNA-seq of Untreated macrophages

growth_protocol: peritoneal exudate cells were washed from the peritoneum 3 days after (.i.p.) thioglycolate injection. Cells were allowed to adhere for 24 hours and non-adherent cells were washed away with several washes of fresh medium. PEC macrophages where treated with IL-10 (100 ng/ml) for 4 hours.

treatment_protocol: Macrophages were treated with 100 ng/ml of IL-10 for four hours. Cells were then harvested with TRIzol and RNA extracted


title: PEC_IL10-treated_STAT3_ChIPseq

description: library insert size: 158

source_name: ChIP in IL-10 treated (4 hours) macrophages against STAT3


title: RNA-seq of IL-10 treated macrophages

description:
library insert size: 188
RNA-seq of IL-10 treated macrophages

source_name: RNA-seq of IL-10 treated macrophages


title: wild-type germinating conidia 8hrs rep1


title: wild-type germinating conidia 6hrs rep1

value: 6 hrs


title: Runx1_uninduced_ChIPseq

status: Public on Feb 10 2012

city: Cambridge

first: Tali

last: Mazor

address: 77 Massachusetts Ave

institute: MIT

data_processing:
Alignment: Raw ChIP-Seq data were processed using the Illumina software pipeline. Only ChIP-Seq reads that aligned to exactly one location in the reference mouse genome were retained (UCSC, mm9)
Peaks:The MACS algorithm (Zhang et al., 200b) was used to identify bound regions by comparing the enrichment of the IP sample against a control IgG IP for background correction. MACS version 1.4.0rc2 was run with all parameters at their default settings.

growth_protocol: L8057 cells were grown in 38.5% IMDM + 38.5% RPMI + 20% FCS + %2 Pen/strep + 1% L-Glutamine,

extract_protocol: The purified DNA was prepared for sequencing on a Beckman Coulter SPRI-TE following manufacturer’s instructions. The seq-prepped DNA was PCR amplified using Illumina primers for 18 cycles. Samples were sequenced on either the Illumina Genome Analyzer II or Illumina Hi-Seq 2000 following the manufacturer's protocols.

treatment_protocol: For induced L8057 cells, 50 nM TPA was added to induced maturation of the cells for 72 hrs. L8057 cells and primary thymocytes were fixed with formaldehyde before sonicated for ChIP.

tag: cell line


title: Tbx20 knockout adult heart, replicate 1

city: Chicago

first: Noboru

middle: Jo

last: Sakabe

state: IL

address: 920 E 58th st

department: Human Genetics

institute: University of Chicago

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9) using Bowtie with options:
-n 2 -m 1 -k 1 --best --strata

source_name: Tbx20 knockout adult heart

growth_protocol: Inducible cardiac-specific Tbx20 kockout mice (Î±-MHC-MerCreMer/Tbx20f/f) were generated by breeding Tbx20f/f mice with mice expressing Cre-recombinase fused to the mutated estrogen receptor MerCreMer under the control of the Î±-MHC promoter (provided by J.D. Molkentin, University of Cincinnati, Cincinnati, Ohio, USA). 6 to 8 week old Î±-MHC-mERCremER/Tbx20f/f male mice were treated with tamoxifen (Sigma-Aldrich, St Louis, Mo) dissolved in sesame oil by intraperitoneal injection once a day for 5 consecutive days at a dosage of 30mg/Kg per day, and used as inducible cardiac-specific Tbx20 knockout mice (âconditional knockout, cKOâ). Control male mice carrying the genotypes Î±- Tbx20f/f or MHC-mER-Cre-mER/Tbx20+/+ were treated with the same tamoxifen regimen.

extract_protocol: Libraries were generated according to Illumina single-end RNA-seq library preparation

value: mixed 129/Black Swiss outbred background

value: whole heart

tag: age

value: 2 months


title: Tbx20 knockout adult heart, replicate 2


title: normal adult heart, replicate 3

source_name: normal adult heart


title: CBFb_uninduced_ChIPseq


title: Runx1_thymocyte_Runx1KO_ChIPseq

value: primary thymocyte

value: Runx1f/f,Vav1-Cre on C57BL/6 background

tag: mouse age

value: 5-8 weeks


title: normal adult heart, replicate 2


title: normal adult heart, replicate 1


title: wild-type germinating conidia 6hrs rep2

value: wild type

value: germinating conidia


title: CBFb_thymocyte_Runx1KO_ChIPseq

tag: cell type


title: Runx1_induced_ChIPseq

description: maturation was induced by adding 50 nM (final concentration) 12-O- tetradecanoylphorbol-13-acetate (TPA) to the medium for 3 days


title: IgG_uninduced_ChIPseq


title: Tbx20 knockout adult heart, replicate 3

tag: strain


title: Ring1b_uninduced_ChIPseq


title: Runx1_thymocyte_control_ChIPseq

value: Runx1f/f on C57BL/6 background


title: IgG_thymocyte_Runx1KO_ChIPseq


title: IgG_thymocyte_control_ChIPseq


title: Ring1b_thymocyte_Runx1KO_ChIPseq


title: Ring1b_thymocyte_control_ChIPseq


title: CBFb_thymocyte_control_ChIPseq


title: Ring1b_alt_ab_ChIPseq


title: IgG_induced_ChIPseq


title: Runx1_for_Ring1b_alt_ab_ChIPseq


title: CD34

first: Julia

last: Salzman

address: 279 West Campus Drive, MC: 5307

data_processing:
Fastq files were mapped to the hg19 refSeq transcript annotation using bowtie with the flags -n 3 and -m 3. Mapped reads are represented in the bowtie file. Reads failing this alignment and also failing alignment ot the UCSC knowngene annotation database were further scrutinized and mapped to a custom database, as described in the main text.

The entire analysis treated the two paired ends as 'single ends' (i.e. aligned/mapped files correspond to single end reads).

source_name: CD34+ cells

extract_protocol: First, 2 or 5ug of total RNA was depleted of ribosomal RNA using the ribo-zero kit (Epicentre, Madison, WI) from the normal hematopoietic and leukemia samples, respectively. RNA was then fragmented to about 350bp using alkaline hydrolysis followed by first and second strand cDNA generation as previously outlined. cDNA was size-selected for a range between 300-500 bp before adaptor ligation to minimize the production of in vitro chimeric transcripts. A second size selection was then performed for 350-600bp to select against chimeric inserts and remove unligated adapters. Libraries were PCR amplified for 15 or 20 cycles for the leukemia and normal hematopoietic samples, respectively. Concentrations were measured using the High Sensitivity DNA Kit for the Bioanalyzer (Agilent, Santa Clara, CA), and samples were then diluted to 10pM. Clusters were generated using the Paired-End Cluster Generation Kit v2 with the cBot according to manufacturers instructions (Illumina, San Diego, CA). The samples were then sequenced on the Illumina Genome Analyzer II using kit v5. All samples were run as a single lane on a 80bp paired-end run (but mate-pairs were uploaded to SRA as single-end runs, resulting in two run files per sample). Leukemia samples were sequenced together, while the remission blood and normal bone marrow subpopulations were a separate run.  Sequencing data will be deposited in GEO.

value: blood


title: neutrophils

source_name: Neutrophils

value: neutrophils


title: CD19

source_name: CD19+ cells


title: Ring1b_induced_ChIPseq


title: CBFb_induced_ChIPseq


title: Input ChIP-seq in Jurkat 2

status: Public on Feb 09 2012

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Jurkat Chromatin Input Control

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to the hg18 build using Eland.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 10bp bins. Counts were normalized to reads per million, and bins with at least 0.5 reads per million are shown.

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: None WCE

value: Jurkat E6-1

tag: cell number


title: RUNX1 ChIP-seq in Jurkat

description: Chromatin IP against RUNX1 in Jurkat

value: Santa Cruz SC-8563

value: 10 million


title: GATA3  ChIP-seq in Jurkat

description: Chromatin IP against GATA3 Jurkat

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

value: Santa Cruz SC-22206

value: 30 million


title: TCF3/E2A ChIP-seq in Jurkat

description: Chromatin IP against E2A Jurkat

value: Santa Cruz SC-349X


title: RUNX1 ChIP-seq in Jurkat 3

description: Chromatin IP against RUNX1 in Jurkat

value: 1 million


title: MCF-7,LTED_ER-ChIP-seq

city: Nashville

first: Todd

middle: W

last: Miller

state: TN

address: 2220 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt Univ

description: Chromatin IP against ERa

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) (Zhang et al., 2008) in Python with the following parameters: effective genome size = 2.7 x 109; band width = 300; model fold = 10,30; p-value cutoff = 10-5; range for calculating regional lambda = 10,000 bp; tag size = 43 bp; maximum duplicate tags at the same position in treatment = 2.

source_name: MCF-7/LTED cells

growth_protocol: Cells were maintained in IMEM + 10% DCC-FBS (no phenol red)

extract_protocol: Lysates were clarified from sonicated nuclei and ER-DNA complexes were isolated with antibody.  Thirty nanograms of ChIP DNA was end-polished with T4 DNA polymerase and kinase. An adenosine base was added to the polished DNA fragments followed by Qiaquick column clean-up. Solexa adaptors were ligated to the ChIP DNA fragments. Samples were run on a 2% e-gel (Invitrogen) for 10 min. A gel region from 200-400 bp was excised (average 300 bp), and DNA was purified using Gel Extraction Kit (Qiagen). Samples were amplified by PCR using 2X Phusion Master Mix and Paired End Primers 1.0 and 2.0 for 18 cycles. Samples were purified using Nucleotide Extraction Kit (Qiagen) and eluted in 12 mL EB Buffer. Samples were then run on a DNA-1000 chip to check the average size of the library prep. All samples had an average size of 300 bp.  Library preps were next subjected to Solexa sequencing using the Genome Analyzer II according to the manufacturer’s instruction.

treatment_protocol: Cells were treated with IMEM + 10% DCC-FBS (no phenol red)

value: Mouse-anti-ER*

value: Neomarkers, clone Ab-10 (TE111.5D11)

tag: catalog #

tag: lot #

value: Rabbit-anti-ER*

tag: Santa Cruz Biotechnology, clone HC-20


title: Input ChIP-seq in Jurkat

description: Jurkat Chromatin Input Control


title: TAL1 ChIP-seq in Jurkat 2

description: Chromatin IP against TAL1 in Jurkat

value: Santa Cruz SC-12984


title: CapH2_Ab1_DMSO_NOT_NORMALIZED_mES_MM8

description:
Chromatin IP against CapH2 in mES cells
Cells were treated for 1 hr with DMSO.

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Bethyl A302-275A

tag: antibody manufacturer

value: Bethyl

tag: treatment

value: DMSO

tag: tiime

value: 1 hr


title: CapH2_Ab1_FLAVO_NOT_NORMALIZED_mES_MM8

description:
Chromatin IP against CapH2 in flavo-treted mES cells
Cells were treated with 1uM flavopiridol for 1hr.

value: 1 uM flavopiridol


title: Smc1_DMSO_NOT_NORMALIZED_mES_MM8

description:
Chromatin IP against Smc1 in mES cells
Cells were treated with DMSo for 1 hr.

value: Bethyl A301-779A


title: CapH2_Ab1_WT_mES_MM8

description: Chromatin IP against CAPH2, a subunit of Condensin II

value: Bethyl A300-275A


title: Smc1_FLAVO_NOT_NORMALIZED_mES_MM8

description:
Chromatin IP against Smc1 in flavo-treated mES cells
Cells were treated with 1uM flavopiridol for 1 hr.


title: TCF12/HEB ChIP-seq in Jurkat

description: Chromatin IP against HEB in Jurkat

value: Santa Cruz SC-357

value: Jurkat E6-1


title: CapH2_Ab2_WT_mES_MM8

value: Bethyl A302-276A


title: TAL1 ChIP-seq in Jurkat 1

description: Chromatin IP against TAL1 in Jurkat

value: 10 million


title: TCRa-1

city: Lausanne

first: Brian

middle: James

last: Stevenson

address: Genopode, UNIL-Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: TCRa mRNA

data_processing:
Each processed data file contains three tab delimited files for each TRAJ gene segment identified by sequencing:
TRAJ*.gnt : in-frame TCRalpha chains containing a uniquely identified TRAV segment
TRAJ*.red : in-frame and out-of-frame TCRalpha chains containing a TRAV segment that could not be uniquely identified
TRAJ*.bnt : out-of-frame TCRalpha chains containing a uniquely identified TRAV segment

source_name: CD8+ thymocytes

growth_protocol: Seven-week-old C57Bl/6 mice were purchased from Harlan laboratory

extract_protocol:
1 mg of total RNA from CD8+ T cell was used for TCR amplification, using specific primer in the constant region fused with the T7 promoter. The in vitro transcription was performed according to the instructions of the MessageAmp II aRNA Amplification Kit (Ambion, Rotkreuz, Switzerland).
Illumina sequencing: A specific ssDNA adapter (adenyl-AGATCGGAAGAGCGGTTCAGddC) was ligated to the 3' end of the RNA fragments using truncated T4 RNA ligase. The first strand cDNA was then synthesized using a primer (CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT) complementary to the ssDNA adapter. The library was prepared by adding the Illumina adapters sequences by PCR amplification using a primer specific to the 5' constant region (AATGATACGGCGACCACCGAGATCTACACAGCAGGTTCTGGGTTCTG) and the standard Illumina PCR primer.

value: CD8+ thymocytes


title: TCRa-2

description: TCRa mRNA


title: HCC-1428,LTED_ER-ChIP-seq

description: Chromatin IP against ERa

source_name: HCC-1428/LTED cells

tag: vendor


title: RUNX1 ChIP-seq in Jurkat 2

description: Chromatin IP against RUNX1 in Jurkat

value: Santa Cruz SC-8563

value: 5 million


title: Normoxic HUVEC_1

status: Public on Feb 07 2012

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: Total RNA was purified using TRIzol (Invitrogen).

data_processing:
Reads with “non called” bases were excluded and the remaining reads were filtered for a minimal quality value of 9 with the SOLiD Software Development Community csfasta_quality_filter.pl script. We also excluded reads mapping to genome coordinates corresponding to any annotated small non-coding RNA comprised in Genbank, RNAdb (v2.0) or NONCODE , in addition to rRNA and tRNA sequences downloaded from Genbank and coding and non-coding RefSeq sequences from UCSC (hg19 assembly). Reads were then mapped against all annotated human miRNA sequences (miRBase v14.0) using SHRiMP. For novel miRNA identification, reads were mapped against the Human hg19 genome sequences using SHRiMP. After alignment quality filtering, reads comprised in miRBase or mapping >3 times to the human genome or overlapping with simple repeats (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/) were removed from the dataset.
Subsequently, after the application of an abundance filter, hits were intersected with a database containing genome-wide short RNA hairpin structure predictions. Only the genomic locations positioned on the stem of a predicted hairpin were accepted for further analysis.

source_name: Human Umbelical Vein Endothelial Cells (HUVEC)

growth_protocol: HUVEC are constituted by a pooled, primary population of human umbelical vein endothelial cells. HUVEC were grown in EGM-2 medium (Lonza) containing 2% FBS in the presence 5% CO2.

extract_protocol: Total and enriched RNA samples were processed into four sequencing libraries using the Small RNA Expression Kit according to the manufacturer’s protocol (SREK Rev. C, Applied Biosystems). Briefly, RNA was first hybridized and ligated with the adapter mix “B”, subsequently reverse transcribed and treated with RNAse H. The obtained cDNA libraries were PCR amplified, purified and size-selected by PAGE, resulting in libraries containing inserted small RNA sequences of 20-40bp length. cDNA libraries were amplified onto beads using emulsion PCR, templated beads were deposited on slides and analyzed using the Applied Biosystems SOLiD™ 3 Sequencer.

treatment_protocol: HUVEC cells were exposed to 1% oxygen for 24 hours using a hypoxic incubator (Forma® Series II 3110 Water Jacketed CO2 Incubator, Thermo Scientific).

value: Human Umbelical Vein Endothelial Cells

tag: oxygen tension

value: atmospheric (about 21%) oxygen tension (normoxia)


title: Hypoxic HUVEC_1

value: 1%  oxygen tension (hypoxia)


title: Hypoxic HUVEC_2

description: Total RNA was purified using TRIzol (Invitrogen) and then enriched for small RNAs up to 60bp by size selection via flashPAGE fractionator (Ambion).


title: Normoxic HUVEC_2


title: SET2_RNASeq_1

status: Public on Feb 08 2012

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

data_processing: After adapter removal reads without adapter and/or with N were discarded, only reads between  15 and 26 nt with base quality of at least 30 and with less than 2 nt with base quality lower than 20 were considered. Reads were mapped using bowtie (only exact matches) to hairpins sequences from miRBase v17 and to human genome sequence (hg19). Reads belonging to unique sequences mapping to more than 5 genomic loci out of miRNA hairpins were discarded. A subsequent phase of accurate mapping of reads to extended hairpins (30 nt before and after hairpin precursor) was performed with bowtie with -best -y -strata options. Reads alignment results were integrated with known miRNA positions to classify reads according to number of mismatches and relative position to known mature miRNA. The raw read count were corrected considering the number of reference sequences showing equally good alignments with the read. Known miRNA quantification and isomiRs characterization is based on exact alignments and on alignments with at most 1 mismatch. New miRNA and moRNA discovery is based only on exact alignments.

source_name: SET2 cell line

extract_protocol: Total RNA was purified using miRNeasy reagents, checked by Agilent, and a small RNA library was generated according to standard Illumina procedure with 5' and 3' SRA adapter ligation. Ligated RNA fragments were reverse transcribed to single-strand cDNA followed by PCR amplification using small RNA primer set.

tag: genotype

value: MUTATED FOR JAK2V617F


title: HSF/D.mel_PB-seq_Rep1_seqA

status: Public on Feb 06 2012

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

data_processing: The PB-seq reads were aligned to the Drosophila Genome (BDGP R5/DM3) using BWA (v 0.5.8c)

organism: Drosophila melanogaster

source_name: HSF IP

growth_protocol: Prior to DNA extraction S2 were cultured as previously described (PMID: 20844575).

extract_protocol: We performed an in vitro binding experiment with purified HSF and naked, sheared genomic Drosophila S2 DNA (PB-seq), to derive an accurate set of potential HSF binding sites in the Drosophila genome.  HSF-bound DNA was specifically eluted and detected by high throughput sequencing.  Drosophila HSF was N-terminally tagged with glutathione s-transferase and a tobacco etch virus (TEV) protease cleavage site.  The C-terminus of the recombinant HSF was fused to the 3xFLAG epitope.  Recombinant HSF was purified from E. coli with glutathione resin as previously described (PMID: 20078429) , with the following modifications:  HSF-3xFLAG elution was achieved by addition of 6xHistidine tagged TEV protease and TEV protease was cleared from the HSF preparation using a Nickel-NTA column.  We incubated 600pM HSF and 2500ng genomic DNA (sonicated to 100-600bp fragment size as previously described in PMID: 20844575) in 1500μl final volume of 1xHSF binding buffer and let it come to equilibrium for an hour at room temperature.  We added 20μl ANTI-FLAG M2 affinity gel for 10 minutes, washed 8 times with 1xHSF binding buffer to remove unbound DNA; 3xFLAG peptide was added to a final concentration of 200ng/μl to specifically elute HSF and HSF-bound DNA.  The mock IP was done in the absence of recombinant HSF.

tag: library strategy

value: PB-Seq

tag: library selection

value: immunoprecipitation

tag: library source

tag: antibody

value: Anti-FLAG M2


title: Input

middle: Paul

last: Seiler

address: 929 E 57th Street

department: Committee on Immunology

description: Sample 3

data_processing:
Reads were mapped to mm9 using Illumina Genome Analyzer Pipeling with default settings. Peaks were called using QuEST (website) under "relaxed" settings using reads which mapped to autosomes and sex chromosomes. Sample 1 uses inputs 1, 4 and 5. Sample 2 uses inputs 1, 2, 3 and 4.
IgG: Reads were aligned with Bowtie using default settings. Wig file was generated using QuEST with default settings.

source_name: input DNA

growth_protocol: NKT cells were isolated from Va14tg mice by paramagnetic enrichment for CD1d-aGC Tetramers.  2x10^7 cells from an average of 10 mice per experiment were collected.

extract_protocol: Purified DNA from Egr2 ChIP and Input were prepared for sequencing following the illumina genomic DNA protocol.  100ng of ChIP DNA from each sample was ligated to Illumina Adaptor Oligo Mix  After 16 cycles of PCR amplification, library fragments between 150-400 bp were purified on a 2% agarose gel.  Gel-purified DNA was further quantified using an Agilent 2100 bioanalyzer.  8 pmoles of DNA library was applied to each lane of the flow cell and sequenced on Illumina GAII sequencer according to standard Illumina protocols.

treatment_protocol: For anti-TCRb injected mice, 3-5 mice were injected with 500ug anti TCRb antibody (clone H57) and thymocytes were collected 24 hours later.  2x10^7 cells were collected and subject to ChIP isolation protocol.

tag: chip antibody


title: IgG

description: Sample 4

data_processing:
IgG.wig; genome build: mm9
Reads were mapped to mm9 using Illumina Genome Analyzer Pipeling with default settings. Peaks were called using QuEST (website) under "relaxed" settings using reads which mapped to autosomes and sex chromosomes. Sample 1 uses inputs 1, 4 and 5. Sample 2 uses inputs 1, 2, 3 and 4.
IgG: Reads were aligned with Bowtie using default settings. Wig file was generated using QuEST with default settings.

tag: strain

value: IgG

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat#

tag: chip antibody lot#


title: VA14tg_NKT

description: Sample 2

data_processing:
Va14tg_NKT.peaks.txt; genome build: mm9
Va14tg_NKT.wig; genome build: mm9
Reads were mapped to mm9 using Illumina Genome Analyzer Pipeling with default settings. Peaks were called using QuEST (website) under "relaxed" settings using reads which mapped to autosomes and sex chromosomes. Sample 1 uses inputs 1, 4 and 5. Sample 2 uses inputs 1, 2, 3 and 4.
IgG: Reads were aligned with Bowtie using default settings. Wig file was generated using QuEST with default settings.

tag: cell type

value: NKT cells were isolated from Va14tg mice

value: anti-EGR2 (Krox-20)

value: Covance


title: no_protein/D.mel_PB-seq_mock_seqA

source_name: mock IP (no HSF)

value: naked, sheared genomic Drosophila S2 DNA


title: Anti-TCRb_inj

description: Sample 1

data_processing:
Anti-TCRb_inj.peaks.txt; genome build: mm9
Anti-TCRb_inj.wig; genome build: mm9
Reads were mapped to mm9 using Illumina Genome Analyzer Pipeling with default settings. Peaks were called using QuEST (website) under "relaxed" settings using reads which mapped to autosomes and sex chromosomes. Sample 1 uses inputs 1, 4 and 5. Sample 2 uses inputs 1, 2, 3 and 4.
IgG: Reads were aligned with Bowtie using default settings. Wig file was generated using QuEST with default settings.

source_name: anti-TCRb injected_thymocytes_EGR2_ChIP

value: thymocytes from anti-TCRb injected mice


title: HSF/D.mel_PB-seq_Rep2_seqB


title: no_protein/D.mel_PB-seq_mock_seqB


title: C24 x Ler methylC

status: Public on Feb 05 2012

city: Canberra

first: Jennifer

last: Taylor

address: Clunies Ross St

department: Plant Industry

country: Australia

institute: CSIRO

data_processing:
Sequence reads were mapped using the BSMAP analysis pipeline (Xi and Li, 2009) using default values.  Mapping was accomplished by using a reiterative single nucleotide trimming of the read until either a successful hit was found or 30 bases had been removed.  An error rate was determined by the number of uniquely mapped methylated C’s to the number of uniquely mapped C’s on the Chloroplast genome.  This equated to above 98% conversion rate. BSMAP output files and README included.
Genome Build:
C24xLer.bsp: TAIR 9

organism: Arabidopsis thaliana

source_name: C24 x Ler methylC

growth_protocol: grown in a 16 hour day cycle at 22°C/18°C (day/night)

extract_protocol: Genomic DNA was extracted using the Dneasy Plant Mini Kit (Qiagen). DNA underwent sonication, end repair and ligation with methylated adapters as per Illumina recommendations for methylSeq. Bisulfite conversion used the Methyl Easy Xceed Kit (Human Genetic Signatures). Bisulfite treated samples were enriched by 18 cycles of PCR.

treatment_protocol: Bisulfite converted DNA using  Methyl Easy Xceed Kit (Human Genetic Signatures)

value: F1 C24 x Ler

tag: tissue

value: Unopened buds


title: Ler methylC

data_processing:
Sequence reads were mapped using the BSMAP analysis pipeline (Xi and Li, 2009) using default values.  Mapping was accomplished by using a reiterative single nucleotide trimming of the read until either a successful hit was found or 30 bases had been removed.  An error rate was determined by the number of uniquely mapped methylated C’s to the number of uniquely mapped C’s on the Chloroplast genome.  This equated to above 98% conversion rate. BSMAP output files and README included.
Genome Build:
Ler.bsp: TAIR 9

source_name: Ler methylC

value: Ler


title: Ler x C24 methylC

data_processing:
Sequence reads were mapped using the BSMAP analysis pipeline (Xi and Li, 2009) using default values.  Mapping was accomplished by using a reiterative single nucleotide trimming of the read until either a successful hit was found or 30 bases had been removed.  An error rate was determined by the number of uniquely mapped methylated C’s to the number of uniquely mapped C’s on the Chloroplast genome.  This equated to above 98% conversion rate. BSMAP output files and README included.
Genome Build:
LerxC24.bsp: TAIR 9

source_name: Ler x C24 methylC

value: F1 LerxC24