title: blastocyste_nanoCage

status: Public on Jan 27 2013

city: ILLKIRCH Cedex

first: Stephanie

last: Le Gras

address: 1, rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Basecalls performed using Illumina pipeline/CASAVA.
Reads without 5' tag were filtered out. The reads containing 5' tags were extracted and trimmed to 25nt, which is the expected size as  a consequence of the Nano-CAGE protocol.
Reads were first mapped to the mouse reference genome (NCBI37/mm9) using Maq v0.7.1 with default parameters except for the number of allowed mismatches (-n) which was set to 3. Positions of the reads uniquely mapped to the mouse genome were cross-compared with the positions of the repeats extracted from UCSC (rmsk table in UCSC database for mus musculus mm9) and reads overlapping a repeat sequence were annotated with the repeat family.
In the second part of the analysis, reads not mapped or multi-mapped to the mouse genome were aligned to RepBase v15.08 repeat sequences for rodent. Reads mapped to a unique repeat family were annotated with the family name.  We added the read counts per repeat family of the two annotation steps and the final read counts were used to estimate the proportion of each type of repeat in several stages.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files prefixed with "repeat" contain reads uniquely aligned to the mouse genome (mm9) and which position overlapped a repetitive element (based on UCSC rmsk table). The ReadCountPerReapeat.txt on the Series record file is a tab separated text file containing the raw number of reads for several types of repetitive elements.

source_name: embryo

extract_protocol: We followed the NanoCAGE protocol described in Plessy et al (2010, Nature Genetics), with some modificationns. Briefly, it is a cap-selection-   based method that allows systematic 5’-end profiling of small quantities of capped RNAs. An exhaustive detailed protocol will be integral part of the publication.

value: embryo

value: F1 (C57BL/6J X CBA/H) crosses

value: Blastocyst stage (92h)


title: oocyte_nanoCage

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: strain

tag: age

value: Oocyte (fully grown)


title: ChREBP fat body knockdown wandering L3 FB_high-sugar diet-reared_biological rep 2

status: Public on Jan 25 2013

city: Saint Louis

first: Thomas

middle: John

last: Baranski

state: MO

address: 660 S. Euclid Ave. Box 8127

country: USA

institute: Washington University School of Medicine

description: Mio/dMondo/dChREBP mutant tissue

data_processing:
To produce bed alignments, sequenced reads were aligned to the D. melanogaster UCSC dm3 assembly using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE MB8 annotation.
Expression was normalized by applying upper-quartile normalization as defined in "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", Bullard et al. BMC Bioinformatics. 2010; 11: 94
Genome_build: MB8
Supplementary_files_format_and_content: Excel worksheet "Matrix" containing normalized RPKM for each raw dataset, indexed by CG (gene)

organism: Drosophila melanogaster

growth_protocol: Animals were reared at 25C on Bloomington Semi-Defined Food with sucrose substituted for glucose (0.15M). High sugar food contained 0.7M sucrose instead of 0.15M.

extract_protocol:
Tripure extraction of total RNA was performed according to the manufacturer's instructions; RNA was DNase-treated and then cleaned on a Qiagen RNeasy column and eluted in RNase-free H2O.
Bar-coded cDNA were prepared from 10 ug total RNA according to a published protocol (Haynes et al, PLoS Pathog 7, e1002411, 2011). 0.15_wt_1 was bar coded with ATCT. 0.15_wt_2:ATCT. 0.15_wt_3:ATCT. 0.15_wt_4:CCAT. 0.15_wt_5:GTGT. 0.15_wt_6:AATT.0.15_wt_1 was bar coded with ATCT. 0.15_wt_2:ATCT. 0.15_wt_3:ATCT. 0.15_wt_4:CCAT. 0.15_wt_5:GTGT. 0.15_wt_6:AATT. 0.15_chr_1: CACT. 0.15_chr_2:CACT. 0.15_chr_3:CACT. 0.7_wt_1: GGTT. 0.7_wt_2: GGTT. 0.7_wt_3:GGTT. 0.7_wt_4:TGCT. 0.7_wt_5:CGGT. 0.7_wt_6:GAAT. 0.7_chr_1:TAGT. 0.7_chr_2: TAGT

treatment_protocol: Animals were reared on control or high sucrose Semi-Defined food from embryo hatch until harvest as wandering L3. Fat bodies were isolated, placed into Tripure, and frozen.

value: fat body

tag: developmental stage

value: wandering third instar larva

tag: Sex

value: female

tag: genotype/variation

value: Mio/dMondo/dChREBP mutant

tag: diet

value: high-sugar diet


title: ChREBP fat body knockdown wandering L3 FB_high-sugar diet-reared_biological rep 1

description: Mio/dMondo/dChREBP mutant tissue


title: wild-type wandering L3 FB_high-sugar diet-reared_biological rep 2

value: wild type


title: ChREBP fat body knockdown, wandering L3 FB_control diet-reared_biological rep 3

description: Mio/dMondo/dChREBP mutant tissue

value: control diet


title: ChREBP fat body knockdown, wandering L3 FB_control diet-reared_biological rep 2

description: Mio/dMondo/dChREBP mutant tissue


title: FUS-mmu_1_KD

city: Baltimore

first: Manolis

last: Maragkakis

state: MD

address: 251 Bayview Blvd

institute: National Institute on Aging

description:
Total RNA minus ribosomal RNA
RNA-Seq KD sample of FUS

data_processing:
The 3’-adaptor was removed from the sequences using the cutadapt software and a 0.25 acceptable error rate for the alignment of the adaptor on the tag.
Reads shorter than 15nt were removed
Reads were aligned to the human (hg19) and mouse (mm9) genomes respectively using BWA with default program parameters
Aligned reads shorter than 20nt that align to more than 1 position on the genome were removed
Aligned reads mapping on repeat elements as defined by RepeatMasker were removed
Peaks were defined by merging overlapping tags into single merged regions and selecting the point with the highest number of aligned reads within each region as the actual peak position. The height of each peak was defined as the total number of tags within the merged region. Only peaks with score higher than 2 were used in further analysis
Genome_build: mm9
Supplementary_files_format_and_content: BED files contain the defined peaks. Scores represent the score of the peaks.
Supplementary_files_format_and_content: The column  names for the bed files are:
Supplementary_files_format_and_content: 1. chromosome       2. start       3. stop       4. name       5. score       6. strand

source_name: Neurons

growth_protocol: Mouse embryonic stem cells (ES) were maintained in ES medium on gelatinized plates without feeder cells. Neuronal differentiation was performed as described previously (Wichterle et al., 2009). Cells were maintained into ADFNB+GDNF.

extract_protocol: Sample preparation for RNA-seq: Total RNA samples from Mouse ES cell derived neurons were extracted with Trizol reagent and treated with DNaseI. Obtained total RNA was fragmented, treated with CIP and then ligated 3' linker. Ligated RNA was captured on streptavidin beads and treated with T4 PNK, and then ligated a 5' linker. 3' and 5' linkers ligated RNA was subject for reverse transcription and double PCR. The PCR products were used for Deep-seq.

treatment_protocol: Solid Support Directional RNA-Seq were performed as previously described (Chi et al., 2009; Vourekas et al., 2012).

tag: cell

value: ES-derived neuronal cells

tag: treatment

value: FUS siRNAs

tag: cell line


title: FUS-mmu_1_CTRL

description:
Total RNA minus ribosomal RNA
RNA-Seq CTRL sample

value: CTRL siRNAs


title: FUS-mmu_2_CTRL


title: wild-type wandering L3 FB_high-sugar diet-reared_biological rep 3


title: FUS-mmu_2

description: HITS-CLIP of FUS prepared from mouse neurons main signal

data_processing:
Library strategy: CLIP-Seq
The 3’-adaptor was removed from the sequences using the cutadapt software and a 0.25 acceptable error rate for the alignment of the adaptor on the tag.
Reads shorter than 15nt were removed
Reads were aligned to the human (hg19) and mouse (mm9) genomes respectively using BWA with default program parameters
Aligned reads shorter than 20nt that align to more than 1 position on the genome were removed
Aligned reads mapping on repeat elements as defined by RepeatMasker were removed
Peaks were defined by merging overlapping tags into single merged regions and selecting the point with the highest number of aligned reads within each region as the actual peak position. The height of each peak was defined as the total number of tags within the merged region. Only peaks with score higher than 2 were used in further analysis
Genome_build: mm9
Supplementary_files_format_and_content: BED files contain the defined peaks. Scores represent the score of the peaks.
Supplementary_files_format_and_content: The column  names for the bed files are:
Supplementary_files_format_and_content: 1. chromosome       2. start       3. stop       4. name       5. score       6. strand

extract_protocol:
Sample preparation for CLIP: Mouse ES cell derived neurons were homogenized and irradiated by UV. Then lyzed, treated with RNaseT1 and DNaseI. Cleared lysates were used for IP with anti-FUS antibody (A300-302) incubated with ProteinA Dynabeads.
The radio-labelled 3' linker was ligated to captured RNA, treated with T4 PNK and separated by SDS-PAGE. Protein-RNA complex was transfered onto nitrocellulose membrane and exposed to X-ray film. Protein-RNA complex was cut out from membrane, treated with ProteinaseK and extracted RNA by Acid Phenol. And then used for 5' linker ligation.P 3' and 5' linkers ligated RNA was subject for reverse transcription and double PCR. The PCR products were used for Deep-seq.

treatment_protocol: High-throughput sequencing of immunoprecipitated and crosslinked RNA  (HITS-CLIP) from mouse neurons was performed using anti-FUS antibody (Bethyl; A300-302A). HITS-CLIP were performed as previously described (Chi et al., 2009; Vourekas et al., 2012).

tag: antibodies

value: FUS (Bethyl Lab, A300-302A)


title: wild-type wandering L3 FB_high-sugar diet-reared_biological rep 1


title: ChREBP fat body knockdown, wandering L3 FB_control diet-reared_biological rep 1

description: Mio/dMondo/dChREBP mutant tissue


title: wild-type wandering L3 FB_high-sugar diet-reared_biological rep 4


title: wild-type wandering L3 FB_control diet-reared_biological rep 2


title: wild-type wandering L3 FB_control diet-reared_biological rep 3


title: FUS-mmu_3_KD


title: FUS-mmu_3_CTRL


title: wild-type wandering L3 FB_control diet-reared_biological rep 1


title: wild-type wandering L3 FB_high-sugar diet-reared_biological rep 5


title: FUS-mmu_2_KD

description:
Total RNA minus ribosomal RNA
RNA-Seq KD  sample of FUS


title: wild-type wandering L3 FB_high-sugar diet-reared_biological rep 6


title: FUS_2

description:
Illumina Genome Analyzer IIe
HITS-CLIP of FUS prepared from human brain-2 (10/8) main signal

data_processing:
Library strategy: CLIP-Seq
The 3’-adaptor was removed from the sequences using the cutadapt software and a 0.25 acceptable error rate for the alignment of the adaptor on the tag.
Reads shorter than 15nt were removed
Reads were aligned to the human (hg19) and mouse (mm9) genomes respectively using BWA with default program parameters
Aligned reads shorter than 20nt that align to more than 1 position on the genome were removed
Aligned reads mapping on repeat elements as defined by RepeatMasker were removed
Peaks were defined by merging overlapping tags into single merged regions and selecting the point with the highest number of aligned reads within each region as the actual peak position. The height of each peak was defined as the total number of tags within the merged region. Only peaks with score higher than 2 were used in further analysis
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain the defined peaks. Scores represent the score of the peaks.
Supplementary_files_format_and_content: The column  names for the bed files are:
Supplementary_files_format_and_content: 1. chromosome       2. start       3. stop       4. name       5. score       6. strand

organism: Homo sapiens

source_name: Temporal cortices

extract_protocol:
Sample preparation for CLIP: Frozen brain tissues were homogenized and irradiated by UV. Then lyzed, treated with RNaseT1 and DNaseI. Cleared lysates were used for IP with anti-FUS antibody (A300-302) incubated with ProteinA Dynabeads.
The radio-labelled 3' linker was ligated to captured RNA, treated with T4 PNK and separated by SDS-PAGE. Protein-RNA complex was transfered onto nitrocellulose membrane and exposed to X-ray film. Protein-RNA complex was cut out from membrane, treated with ProteinaseK and extracted RNA by Acid Phenol. And then used for 5' linker ligation.P 3' and 5' linkers ligated RNA was subject for reverse transcription and double PCR. The PCR products were used for Deep-seq.

treatment_protocol: High-throughput sequencing of immunoprecipitated and crosslinked RNA  (HITS-CLIP) from normal human brain was performed using anti-FUS antibody (Bethyl; A300-302A). HITS-CLIP were performed as previously described (Chi et al., 2009; Vourekas et al., 2012).

value: Human Brain


title: FUS_3

description:
Illumina Genome Analyzer IIe
HITS-CLIP of FUS prepared from human brain-1 (7/16) main signal


title: 8cells_nanoCage

value: 8 cell stage (68h)


title: wild-type wandering L3 FB_control diet-reared_biological rep 5


title: FUS_1

description:
Illumina Genome Analyzer IIe
HITS-CLIP of FUS prepared from human brain-3 (10/15) main signal


title: wild-type wandering L3 FB_control diet-reared_biological rep 4


title: 2cells_nanoCage

value: embryo

value: 2 cell stage (48h)


title: FUS-mmu_1


title: 3T3-8hrs-mild-HS-Riboseq

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

data_processing:
RNAseq: mapping was performed using bowtie v. 12.3 with the following parameters: "-m 1 --best --strata -m 1 -n 2 --best --strata --sam" with a sam format output. reads were uniquely mapped to the mm9 genome, with the addition of splice junctions and ribosomal RNA. the 2 ends of each library were further combined to a single sam file.  RNA Seq bowtie files for the combined replicates of control, HS8M, and HS2S are provided as supplementary files on the Series record.
Riboseq: first, reads were trimmed to a length of 32, then polyAs were further trimmed off. reads with lengthes of 22-32 were seperately uniquely mapped to the same genome file using bowtie, and the output sam files were unified to create a single sam file for each sample.

source_name: 3T3 cells

extract_protocol:
RNAseq- RNAeasy for RNA extraction and standard illumina PE including size selection. Riboseq - RNA extraction and library prepration as described in Ingolia et al. Science, 2009
Avg insert size and std for PE libraries: Control_RNA1&2 - 155 & 12.5; HS8M_RNA1&2 - 182 & 10.3; HS2S_RNA1&2 - 158 & 9.6

treatment_protocol: Mild HS: 8 hours in 42 deg C, Severe HS: 2 hours in 44 deg C.

value: mild heat shock

value: 3T3 cells

tag: assay type

value: Riboseq


title: ES-nonWGA-H3K4me3

status: Public on Jan 24 2013

city: Singapore

first: Vibhor

last: Kumar

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

country: Singapore

institute: Genome Institute of Singapore

description: wiggle track without GC bias correction

library_source: genomic

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CME106-H3K4me3.vstep.wig: mm8

molecule: genomic DNA

source_name: Embryonic stem cell

growth_protocol: Gonads were microscopically dissected from embryonic day 11.5 and 13.5 embryos, which were derived from the cross between male homozygous Pou5f1-GFP mice (Jackson’s lab, stock no. 004654) and female wild type CD1 mice.

extract_protocol: ChIP assays were performed as described previously (Loh et al., 2006). Cells were crosslinked with 1% formaldehyde for 8 min at room temperature and the formaldehyde was quenched with 125 mM glycine. FACS-purified cells were fixed, quenched and rinsed with TBSE buffer twice before storage at -80 degree Celsius until sufficient cell numbers are accumulated for ChIP experiments. Cell lysates were sonicated using the bioruptor (Diagenode) and chromatin extracts were immunoprecipitated with anti-H3K4me3 (04-745, Millipore), anti-H3K27me3 (07-449, Millipore), anti-H3K27ac (ab4729, Abcam) and H2BK20ac (ab52988, Abcam) antibodies. Following de-crosslinking, small-scale ChIP samples were subjected to an additional 15 cycles of amplification using the GenomePlex Single Cell Whole Genome Amplification Kit (WGA4, Sigma) and further purified using the QIAquick PCR purification kit. For all ChIP experiments, quantitative PCR analyses were performed in real-time using the ABI PRISM 7900 Sequence Detection System and SYBR Green Master Mix. Relative occupancy values were determined by calculating the immunoprecipitation efficiency (ratios of the amount of immunoprecipitated DNA to that of the input sample). For ChIP-Seq library preparation (ChIP-Seq DNA Sample Prep Kit IP-102-1001, Illumina), 5-15 ng of ChIP DNA was used for end-repair and adaptor ligation followed by 15 cycles of amplification. 200-300 bp size fragments were selectively cut from the agarose gel and purified using the Qiagen gel extraction kit. Small-scale ChIP samples were subjected to additional processing steps to excise PCR adaptors prior to ChIP-Seq library preparation. The extracted DNA was quantified using Picogreen assay and subjected to ChIP-Seq sequencing for 36 cycles according to the manufacturer’s instructions (Illumina).

treatment_protocol: Gonads were treated with 0.25% Trypsin-EDTA (Gibco) for 10-15 min at 37 C, and trypsin was inactivated by addition of 15% Fetal Bovine Serum (FBS)/ DMEM (Gibco). Cells were filtered through 40 µm cell strainers (BD Falcon) to obtain single cell suspension for FACS sorting (FACSAria II SORP, BD Bioscience).

value: Embryonic stem cell

tag: ChIP

value: H3K4me3 (04-745, Millipore)


title: TAF15_3_L

description:
HITS-CLIP of TAF15 prepared from human brain-3 main signal
Illumina Genome Analyzer IIe

data_processing:
The 3’-adaptor was removed from the sequences using the cutadapt software and a 0.25 acceptable error rate for the alignment of the adaptor on the tag.
Reads shorter than 15nt were removed
Reads were aligned to the human (hg19) and mouse (mm9) genomes respectively using BWA with default program parameters
Aligned reads shorter than 20nt that align to more than 1 position on the genome were removed
Aligned reads mapping on repeat elements as defined by RepeatMasker were removed
Peaks were defined by merging overlapping tags into single merged regions and selecting the point with the highest number of aligned reads within each region as the actual peak position. The height of each peak was defined as the total number of tags within the merged region. Only peaks with score higher than 2 were used in further analysis
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain the defined peaks. Scores represent the score of the peaks.
Supplementary_files_format_and_content: The column  names for the bed files are: 1. chromosome       2. start       3. stop       4. name       5. score       6. strand

extract_protocol: Sample preparation for HITS-CLIP: Frozen brain tissues were homogenized and irradiated by UV. Cells were lysed, treated with RNaseT1 and DNaseI. Cleared lysates were used for IPs using anti-TAF15 antibodies (A300-308A) that were cojugated with ProteinA Dynabeads.

treatment_protocol: High-throughput sequencing of immunoprecipitated and crosslinked RNA  (HITS-CLIP) from normal human brain was performed using anti-TAF15 antibody (Bethyl; A300-308A). HITS-CLIP was performed as previously described (Chi et al., 2009; Vourekas et al., 2012).

value: Temporal cortex

tag: origin

value: Brain

value: TAF15 (Bethyl Lab, A300-308A)


title: wild-type wandering L3 FB_control diet-reared_biological rep 6

value: fat body

value: wandering third instar larva

value: female

value: wild type

value: control diet


title: ES-nonWGA-input

description: wiggle track without GC bias correction

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CME105-input.vstep.wig: mm8

value: none, input-DNA


title: Replicate-1-e13.5PGC-H3K4me3

description: The provided wiggle track of ChIP-seq from germ cells is made after GC bias correction using input DNA library

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e13.5-rep1-H3K4me3.vstep.wig: mm8

source_name: FACS-purified Pou5f1-GFP-positive germ cells

value: Embryonic day 13.5 male-gonad

value: (CBA/CaJ X C57BL/6J)F16+ X Hsd:ICR(CD-1)


title: Replicate-1-e13.5PGC-H2BK20ac

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e13.5-rep1-H2BK20ac.vstep.wig: mm8

value: H2BK20ac (ab52988, Abcam)


title: Replicate-1-e13.5PGC-H3K27ac

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e13.5-rep1-H3K27ac.vstep.wig: mm8

value: H3K27ac (ab4729, Abcam)


title: e11.5PGC-H3K4me3

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e11.5-H3K4me3.vstep.wig: mm8

value: Embryonic day 11.5 gonad


title: Replicate-2-e13.5PGC-input, 3

description: wiggle track without GC bias correction

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CMG009-CMG010-e13.5-rep2-Input.vstep.wig: mm8


title: Replicate-2-e13.5PGC-H3K27me3

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e13.5-rep2-H3K27me3.vstep.wig: mm8

value: H3K27me3 (07-449, Millipore)


title: e11.5PGC-control, 2

description: wiggle track without GC bias correction

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CMG018-e11.5-Input.vstep.wig: mm8


title: Replicate1-ES-WGA-input

description: wiggle track without GC bias correction

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CMG017-WGA-r1-input.vstep.wig: mm8

value: Embryonic stem cell


title: Replicate-2-e13.5PGC-H3K4me3

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e13.5-rep2-H3K4me3.vstep.wig: mm8

value: H3K4me3 (04-745, Millipore)


title: e11.5PGC-H3K27me3

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e11.5-H3K27me3.vstep.wig: mm8


title: TAF15_2_L

description:
HITS-CLIP of TAF15 prepared from human brain-2 main signal
Illumina Genome Analyzer IIe

value: Temporal cortex


title: e11.5PGC-control, 1

description: wiggle track without GC bias correction

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CMG007-e11.5-Input.vstep.wig: mm8


title: TAF15_3_H

description:
HITS-CLIP of TAF15 prepared from human brain-3 higher signal
Illumina Genome Analyzer IIe

value: Brain


title: Replicate-2-e13.5PGC-input

description: wiggle track without GC bias correction

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CMG021-e13.5-rep2-Input.vstep.wig: mm8


title: Replicate-1-e13.5PGC-input, 2

description: wiggle track without GC bias correction

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CMG003-e13.5-rep1-Input.vstep.wig: mm8


title: e11.5PGC-H3K27ac

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e11.5-H3K27ac.vstep.wig: mm8


title: Replicate-2-e13.5PGC-H2BK20ac

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e13.5-rep2-H2BK20ac.vstep.wig: mm8


title: TAF15_2_H

description:
HITS-CLIP of TAF15 prepared from human brain-2 higher signal
Illumina Genome Analyzer IIe

data_processing:
The 3’-adaptor was removed from the sequences using the cutadapt software and a 0.25 acceptable error rate for the alignment of the adaptor on the tag.
Reads shorter than 15nt were removed
Reads were aligned to the human (hg19) and mouse (mm9) genomes respectively using BWA with default program parameters
Aligned reads shorter than 20nt that align to more than 1 position on the genome were removed
Aligned reads mapping on repeat elements as defined by RepeatMasker were removed
Peaks were defined by merging overlapping tags into single merged regions and selecting the point with the highest number of aligned reads within each region as the actual peak position. The height of each peak was defined as the total number of tags within the merged region. Only peaks with score higher than 2 were used in further analysis
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain the defined peaks. Scores represent the score of the peaks.
Supplementary_files_format_and_content: The column  names for the bed files are: 1. chromosome       2. start       3. stop       4. name       5. score       6. strand

value: TAF15 (Bethyl Lab, A300-308A)


title: Replicate-1-e13.5PGC-input, 1

description: wiggle track without GC bias correction

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CMG001-e13.5-rep1-Input.vstep.wig: mm8


title: Replicate-2-e13.5PGC-H3K27ac

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e13.5-rep2-H3K27ac.vstep.wig: mm8


title: TAF15_1_L

description:
HITS-CLIP of TAF15 prepared from human brain-1 main signal
Illumina Genome Analyzer IIe


title: TAF15-mmu_3_KD

description:
RNA-Seq KD sample of TAF15
Total RNA minus ribosomal RNA

data_processing:
The 3’-adaptor was removed from the sequences using the cutadapt software and a 0.25 acceptable error rate for the alignment of the adaptor on the tag.
Reads shorter than 15nt were removed
Reads were aligned to the human (hg19) and mouse (mm9) genomes respectively using BWA with default program parameters
Aligned reads shorter than 20nt that align to more than 1 position on the genome were removed
Aligned reads mapping on repeat elements as defined by RepeatMasker were removed
Peaks were defined by merging overlapping tags into single merged regions and selecting the point with the highest number of aligned reads within each region as the actual peak position. The height of each peak was defined as the total number of tags within the merged region. Only peaks with score higher than 2 were used in further analysis
Genome_build: mm9
Supplementary_files_format_and_content: BED files contain the defined peaks. Scores represent the score of the peaks.
Supplementary_files_format_and_content: The column  names for the bed files are: 1. chromosome       2. start       3. stop       4. name       5. score       6. strand

extract_protocol: Sample preparation for RNA-seq: Total RNA samples from Mouse ES cell-derived neurons were extracted with Trizol reagent and treated with DNaseI and Ribo-minus kit to remove ribosomal RNAs.

treatment_protocol: Solid Support Directional RNA-Seq was performed as previously described (Chi et al., 2009; Vourekas et al., 2012).

tag: cell type

value: Neuron

value: ES-derived neuronal cells

value: TAF15 siRNAs


title: Replicate-1-e13.5PGC-H3K27me3

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-GCcor-e13.5-rep1-H3K27me3.vstep.wig: mm8


title: TAF15-mmu_2_KD

description:
RNA-Seq KD  sample of TAF15
Total RNA minus ribosomal RNA


title: Replicate1-ES-WGA-H3K4me3

description: wiggle track without GC bias correction

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
genome build: mm8
Genome Build:
track-CME102WGA-r1-H3K4me3.vstep.wig: mm8


title: TAF15-mmu_2_CTRL

description:
RNA-Seq CTRL sample
Total RNA minus ribosomal RNA

value: CTRL siRNAs


title: TAF15-mmu_1_CTRL


title: TAF15-mmu_1_KD


title: TAF15-mmu_1

description: HITS-CLIP of TAF15 prepared from mouse neurons main signal.

extract_protocol:
High-throughput sequencing of immunoprecipitated and crosslinked RNA  (HITS-CLIP) from mouse neurons was performed using anti-TAF15 antibody (Bethyl; A300-308A).
HITS-CLIP was performed as previously described (Chi et al., 2009; Vourekas et al., 2012).


title: TAF15-mmu_2

treatment_protocol: High-throughput sequencing of immunoprecipitated and crosslinked RNA  (HITS-CLIP) from mouse neurons was performed using anti-TAF15 antibody (Bethyl; A300-308A). HITS-CLIP was performed as previously described (Chi et al., 2009; Vourekas et al., 2012).


title: RNA Polymerase II 24h

city: Copenhagen

first: Johannes

middle: Eichler

last: Waage

address: Ole Maaløesvej 5

department: Biotech Research and Innovation Center

country: Denmark

institute: University Of Copenhagen

data_processing:
>> Mapping (all) <<
Bowtie v. 0.12.7
Standard settings
Normalisation to sequencing depth (all)
Fragment extension to 200bp, sonication fragment length (all)
>> Peak calling (CEBP) <<
uSeq
Settings: window 177bp, peakshift 131bp, DFR=1%, log2ratio 1.3
Igg used as control
>> Peak calling (Egr1) <<
MACS v 1.4.1
P=1E-9
Igg used as control
Genome_build: mm9
Supplementary_files_format_and_content: Bed files representing called peaks for CEBPA/CEBPB. For Pol-II, normalized RPKM counts to longest refseq-genebody

source_name: RNA Polymerase II 24h

extract_protocol:
Livers from five individual mice for each time point were harvested, directly snap-frozen in liquid nitrogen and stored at -80oC
ChIP was performed as described earlier (Sandmann et al. 2006a).

treatment_protocol: The partial hepatectomy was performed on WT mice (C57BL6/J, male, 7 weeks old) by removing three of five liver lobes as described earlier (Thoren et al. 2010), using the resected liver tissue as 0 hr time point.

tag: antibody

value: RNA Polymerase II

tag: time point

value: 7 weeks old

tag: gender

value: male

value: Total hepatectomized liver

tag: antibody cat#/vendor

value: AC-055-100, Daigenode


title: RNA Polymerase II 16h

source_name: RNA Polymerase II 16h

tag: strain

tag: age

tag: tissue


title: RNA Polymerase II 48h

source_name: RNA Polymerase II 48h


title: TAF15-mmu_3_CTRL


title: C/EBPbeta 36h

source_name: C/EBPbeta 36h

value: C/EBPbeta

value: Sc-150, Santa Cruz


title: RNA Polymerase II 0h

source_name: RNA Polymerase II 0h


title: C/EBPbeta 48h

source_name: C/EBPbeta 48h


title: C/EBPbeta 24h

source_name: C/EBPbeta 24h


title: L267

city: Bruxelles

first: Nicolas

last: Rosewick

address: 121 Boulevard de Waterloolaan

department: Insitut Jules Bordet

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Base calling performed with CASAVA 1.8.
Adapter trimming and quality filtering was perfomed using cutadapt (param : -m 15).
Reads were aligned using bowtie 0.12.7 (param : --best ) using a reference genome composed of Ovis aries genome OAR 2.0 and home sequenced BLV genome (very similar to NC_001414.1).
Read count was performed using htseq-count
Read count normalization was performed using DESeq (Simon Anders, Wolfgang Huber:Differential expression analysis for sequence count data  Genome Biology(2010))
Genome_build: Reference genome composed of Ovis aries genome OAR 2.0 and home sequenced BLV genome (very similar to NC_001414.1).
Supplementary_files_format_and_content: Tab-delimited text file include abundance measurements [raw read count and normalized count] for every sample.

organism: Ovis aries

source_name: B-Cell line, BLV-infected,  lymphoma

extract_protocol:
Trizol
Illumina Small-RNA v1.5 Sample prep kit

value: B-cell

tag: virus

value: Bovine Leukemia Virus


title: RNA Polymerase II 36h

source_name: RNA Polymerase II 36h


title: RNA Polymerase II 168h

source_name: RNA Polymerase II 168h


title: IgG Mock 0h

source_name: IgG Mock 0h

value: IgG Mock

value: Sigma I8140


title: 395t0

source_name: B-cells, BLV-infected, leukemic


title: RNA Polymerase II 3h

source_name: RNA Polymerase II 3h


title: C/EBPbeta 168h

source_name: C/EBPbeta 168h


title: Egr1 36h

source_name: Egr1 36h

value: Sc-110x, Santa Cruz


title: YR2

source_name: B-Cell line, BLV-infected,  leukemic


title: C/EBPbeta 8h

source_name: C/EBPbeta 8h


title: 2531L


title: C/EBPbeta 3h

source_name: C/EBPbeta 3h


title: 267t0

source_name: B-cells, BLV-infected, lymphoma


title: C/EBPbeta 16h

source_name: C/EBPbeta 16h


title: 2241L


title: C/EBPbeta 0h

source_name: C/EBPbeta 0h


title: C/EBPalpha 168h

source_name: C/EBPalpha 168h

value: C/EBPalpha

value: Sc-61, Santa Cruz


title: 2241A1

source_name: B-cells, BLV- infected cells isolated from asymptomatic sheep


title: RNA Polymerase II 8h

source_name: RNA Polymerase II 8h


title: 2532A


title: C/EBPalpha 36h

source_name: C/EBPalpha 36h


title: C/EBPalpha 48h

source_name: C/EBPalpha 48h


title: Non-WGA-ES-H3K27me3

description: wiggle track made after GC bias correction and convolution with peak-detection kernel

data_processing:
All the ChIP-Seq and input control tag data were binned in form of 200 bp bins. GC bias correction was done for ChIP-Seq data using respective input controls. Peak detection was done on binned GC-corrected signal after convolving it with a kernel just as in F-Seq, however here, kernels were first learned using enriched regions for each ChIP-Seq data. ChIP-Seq peaks overlapping repeats (RNA repeats, Satellites and segmental duplications) and peaks in input control were removed as false positives.
Genome_build: mm8

source_name: Embryonic stem cell

treatment_protocol: Gonads were treated with 0.25% Trypsin-EDTA (Gibco) for 10-15 min at 37 C, and trypsin was inactivated by addition of 15% Fetal Bovine Serum (FBS)/ DMEM (Gibco). Cells were filtered through 40 µm cell strainers (BD Falcon) to obtain single cell suspension for FACS sorting (FACSAria II SORP, BD Bioscience).

value: Embryonic stem cell

value: H3K27me3 (07-449, Millipore)


title: C/EBPalpha 8h

source_name: C/EBPalpha 8h


title: C/EBPalpha 24h

source_name: C/EBPalpha 24h


title: C/EBPalpha 3h

source_name: C/EBPalpha 3h


title: 100kCells-ES-input-WGA

description: wiggle track without GC bias correction

tag: number of cells

value: 100k Cells

value: none, input-DNA


title: Non-WGA-ES-input

description: wiggle track without GC bias correction


title: C/EBPalpha 16h

source_name: C/EBPalpha 16h

value: 7 weeks old


title: 1kCells-ES-H3K27me3-WGA

value: 1k Cells


title: 10kCells-ES-input-WGA

description: wiggle track without GC bias correction

value: 10k Cells


title: Replicate2-ES-WGA-H3K4me3

description: wiggle track without GC bias correction

value: H3K4me3 (04-745, Millipore)


title: 1kCells-ES-input-WGA

description: wiggle track without GC bias correction


title: striated_muscle_LMNA_KO_1

status: Public on Jan 28 2013

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

data_processing:
demultiplexing and barcode clipping
quality filtering
mapping with tophat1.2.0, USCS known genes, mm9
cuffdiff0.0.5
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_values.xls;normalized expression values used for assessment of differential gene expression, only one fpkm value is calculated per sample type

source_name: striated muscle

extract_protocol: total RNA was isolated by the TRIZOL method and purified with RNeasy kit. NUGEN ovation RNA-Seq (samples 1-6) and NUGEN complete RNA-Seq protocol (samples 7-12)

tag: sample type

value: striated muscle

tag: genotype/variation


title: Tot2, MSCV-IRF8, Day3, anti-PU.1

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

data_processing:
Basecalls performed using CASAVA version 1.7
Tag sequences were mapped on mouse genome sequences (mm9) by the Bowtie software with optional parameters “-a --best --strata -m 1 -v 2 -S mm9”.
Peaks were identified using the FindPeaks tool in the HOMER package with input DNA tags as background distribution, or identified using SICER (optional parameters “mm9 1 200 200 0.74 200 .01”) with input DNA tags as background distribution.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files reporting ChIP-Seq peaks with input DNA tags as background distribution

source_name: Tot2 cells, MSCV-IRF8 transduced, Day3

growth_protocol: Myeloid progenitor cell line Tot2 cells derived from Irf8 knockout mouse were cultured in RPMI1640 supplemented with 2 mM L-Glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 20% fetal bovine serum and 5.0 ng/ml granulocyte-macrophage colony stimulating factor.

extract_protocol: The lysates were sonicated and immunoprecipitation was then performed using anti-IRF8 antibody, anti-PU.1 antibody or anti-H3K4me1 antibody, coupled with magnetic Dynabeads-Protein A. Purified ChIP DNA was modified for end repair, adapter ligation and then separated by agarose gel electrophoresis to select DNA fragments between 170 and 230 bp. Gel-purifed DNA was amplified by PCR for ChIP-Seq library preparation according to the Illumina’s manuals. After verifying the qualities by Bioanalyzer (Agilent), eight pmol of each ChIP-Seq library was used directly for cluster generation on Cluster Station (Illumina). The sequencing analysis by Genome Analyzer IIx (Illumina) was performed according to the manufacturer’s manuals.

treatment_protocol: Retroviral preparation and transduction with control MSCV or MSCV-IRF8 were performed as described previously (Tamura et al. Blood 106: 1938, 2005). Cells were transduced by spinoculation in a retroviral supernatant supplemented with cytokines and 4 μg/ml polybrene. At 3 days after the transduction, the cells were harvested for chromatin immunoprecipitation.

value: Myeloid progenitor cells

tag: culture condition

value: MSCV-IRF8 transduced

tag: treatment period

value: 3 days

tag: chip antibody

value: rabbit anti-PU.1 antibody (sc-352, Santa Cruz)


title: Replicate2-ES-WGA-input

description: wiggle track without GC bias correction

tag: ChIP


title: 10kCells-ES-H3K27me3-WGA


title: Tot2, MSCV-IRF8, Day3, anti-IRF8

data_processing:
Basecalls performed using CASAVA version 1.７
Tag sequences were mapped on mouse genome sequences (mm9) by the Bowtie software with optional parameters “-a --best --strata -m 1 -v 2 -S mm9”.
Peaks were identified using the FindPeaks tool in the HOMER package with input DNA tags as background distribution, or identified using SICER (optional parameters “mm9 1 200 200 0.74 200 .01”) with input DNA tags as background distribution.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files reporting ChIP-Seq peaks with input DNA tags as background distribution

source_name: Tot2 cells, MSCV-IRF8 transuced, Day3

extract_protocol: The lysates were sonicated and immunoprecipitation was then performed using anti-IRF8 antibody or anti-H3K4me1 antibody, coupled with magnetic Dynabeads-Protein A. Purified ChIP DNA was modified for end repair, adapter ligation and then separated by agarose gel electrophoresis to select DNA fragments between 170 and 230 bp. Gel-purifed DNA was amplified by PCR for ChIP-Seq library preparation according to the Illumina’s manuals. After verifying the qualities by Bioanalyzer (Agilent), eight pmol of each ChIP-Seq library was used directly for cluster generation on Cluster Station (Illumina). The sequencing analysis by Genome Analyzer IIx (Illumina) was performed according to the manufacturer’s manuals.

tag: cell line

value: Myeloid progenitor cell line Tot2 (derived from Irf8 knockout mouse)

value: goat anti-IRF8 antibody (C-19; Santa Cruz Biotechnology)


title: Tot2, MSCV-IRF8, Day3, input DNA


title: Tot2, MSCV-IRF8, Day3, anti-H3K4me1

value: rabbit anti-H3K4me1 antibody (Ab8895, Abcam)


title: Tot2, MSCV, Day3, anti-H3K4me1

source_name: Tot2 cells, MSCV transuced, Day3

value: MSCV transduced


title: HM-1:IMSS AGO2-2 small RNA

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

data_processing:
Basecalling was performed using 454 Sequencing Data Analysis software
Adaptor sequences were removed from each read
Duplicate sequences were removed
Unique reads were filtered by removing all reads that mapped to E. histolytica tRNA, rDNA, LINES and SINES
Filtered reads were mapped to the E. histolytica genome using bowtie with the parameters: -v 1 -k 5
Genome_build: E. histolytica HM-1:IMSS, version 2009-11-27 (http://amoebadb.org/)
Supplementary_files_format_and_content: fasta files are unique reads after adaptor removal
Supplementary_files_format_and_content: txt files are bowtie output.
Please note: Library preparation method is strand specific. Check adaptor sequence for orientation (5' adaptor = CCTGAAA; 3' adaptor = CTGTAGG)

organism: Entamoeba histolytica

source_name: E. histolytica HM-1:IMSS

growth_protocol: E. histolytica was grown in standard axenic culture conditions

extract_protocol: For the EhAGO2-2 IP RNA library, RNA was extracted from the IP material, directly ligated to the 3´-adapter oligonucleotide, size fractionated and treated with CIP and PNK, and then ligated to the 5´-adapter oligonucleotide. For the Rahman small RNA library, 100ug of small RNA enriched RNA was size-fractionated on a 12% TBE urea polyacrylamide gel, the 15-30nt fraction was excised, followed by 3´-adapter ligation, CIP+PNK treatment, and 5´-adapter ligation as above.For both libraries, the final ligated RNA with both 5´- and 3´-adapters was converted to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen, CA, USA). The cDNA was PCR-amplified using 454 Primers (A and B) and 20 cycles, and resolved on a 4% low melting point agarose gel. The band at 100bp was excised and purified, and then further heat-denatured and purified from a 6% PAGE-urea gel. After a second round of purification, the recovered DNA was resuspended in Qiagen elution buffer, and pipelined into the 454 sequencing procedure.

tag: isolation method

value: Myc-tagged EhAGO2-2 IP

value: anti-Myc (Pierce)


title: Rahman small RNA

source_name: E. histolytica Rahman

value: size selection (15-40nt)

value: Rahman

tag: antibody


title: Tot2, MSCV, Day3, input DNA


title: Pooled Mangrove

status: Public on Jan 23 2013

city: Thuwal

first: Pugalenthi

last: Ganesan

address: Ibn AlHaythamm Bldg

department: Division of Biological and Environmental Sciences and Engineering

country: Saudi Arabia

institute: king abdullah university of science and technology

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalls
Sequenced reads were trimmed for adaptor sequence and low-complexity or low-quality sequence reads were removed
Sequences outside 18-25 nucleotide length are removed
Reads that perfectly match rRNA,tRNA, snRNAs reported in Rfam database are removed
Only reads that have exact match with mangrove cDNA sequences deposited in Mangrove Transcriptome Database (http://mangrove.illinois.edu/ were retained. Non matching reads were discarded.
Supplementary_files_format_and_content: Tab-delimited text file containing small RNAs and their abundance

organism: Avicennia marina

extract_protocol:
Total RNA was extracted from several mangrove tissues (roots, stems, leaves, buds, flowers, and seeds) using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions.
The mangrove small RNA library was prepared with TruSeq Small RNA Sample Prep Kit (Illumina, Inc.) using the illumina TruSeq small RNA sample preparation protocol according to the manufacturer’s instructions. Briefly, the RNA 3’ adapter was modified to target miRNAs and other small RNAs that had a 3’ hydroxyl group resulting from DCL cleavage.

value: pooled roots, stems, leaves, buds, flowers, and seeds


title: 2241A0

tag: cell type

value: B-cell

value: Bovine Leukemia Virus


title: PC3 [RRBS]

city: Ghent

first: Tim

last: De Meyer

address: Coupure Links 653

department: Dept. of Mathematical Modelling, Statistics and Bioinformatics

institute: Ghent University

description: Sample 18

data_processing:
RRBS: Data preprocessing, including alignment, was performed by BaseClear's proprietary algorithms (http://www.baseclear.com/dna-sequencing/next-gen-sequencing/epiquest-5-mc-analysis/basic-service/)
RRBS: Data were summarized into file where for each CpG assessed by RRBS both the coverage (amount of alleles sequenced) and amount of methylated alleles for that specific CpG are mentioned. Amounts of alleles sequenced and methylated were summed for both strands.
Supplementary_files_format_and_content: RRBS .txt file with columns containing resp. line number, chromosome, start and end position CpG, amount of alleles methylated, amount of alleles assessed (= coverage for specific CpG).  Txt file containing amounts of methylated alleles and total alleles measured per CpG that was assessed by RRBS (summed for both strands).
Genome_build: HG19

source_name: Prostate cancer cell line

growth_protocol: ATCC complete growth medium

extract_protocol:
RRBS was performed  by BaseClear (Leiden, NL) using their EpiQuest DNA Methylation Analysis Platform (http://www.baseclear.com/dna-sequencing/next-gen-sequencing/epiquest-5-mc-analysis/).
Easy DNA kit (Invitrogen K1800-01)

value: PC3 (purchased from ATCC)

tag: assay

value: RRBS


title: C/EBPalpha 0h

source_name: C/EBPalpha 0h

value: C/EBPalpha

tag: time point

value: 7 weeks old

tag: gender

value: male

value: Total hepatectomized liver

tag: antibody cat#/vendor

value: Sc-61, Santa Cruz


title: DU145 [RRBS]

description: Sample 17

value: DU145 (purchased from ATCC)


title: 100kCells-ES-H3K27me3-WGA

tag: tissue

value: Embryonic stem cell

value: 100k Cells

tag: strain

value: H3K27me3 (07-449, Millipore)


title: DU145 [MBD MethylCap]

description: Sample 11

data_processing:
MBD: Data were mapped using BOWTIE (--phred64-quals -a -X400 -n0 -m1 -p16)
MBD: Data were summarized into file where each line includes the chromosome, the beginning and end position of a stretch of that chromosome with the same amount of mapped fragments, and the amount of mapped fragments
Supplementary_files_format_and_content: MBD .txt file with columns containing resp. line number, chromosome, start and end position (nucleotide) and amount of mapped fragments.  Txt file containing intensities per nucleotide (summarized).
Genome_build: HG19

extract_protocol:
MBD-capturing by MethylCollector, MethylCollector Ultra, MethylCap, MethylMiner, or MethylMagnet.  For MBD-seq, libraries were prepared using standard multiplexed paired-end Chip-seq protocol.
Easy DNA kit (Invitrogen K1800-01)

value: MBD

tag: mbd-capturing by kit

value: MethylCap


title: PC3 [MBD MethylCap]

description: Sample 12


title: PC3 [MBD MethylCollector Ultra]

description: Sample 9

value: MethylCollector Ultra


title: HCT15 [MBD MethylCap]

description: Sample 10

source_name: Colorectal carcinoma cell line

value: HCT15 (purchased from ATCC)


title: DU145 [MBD MethylMiner]

description: Sample 14

value: MethylMiner


title: PC3 [MBD MethylCollector]

description: Sample 6

value: MethylCollector


title: HCT15 [MBD MethylCollector]

description: Sample 4


title: DU145 [MBD MethylCollector]

description: Sample 5


title: DU145 [MBD MethylCollector Ultra]

description: Sample 8


title: DJ2

status: Public on Jan 22 2013

city: Shenzhen

first: Maoshan

last: Chen

state: Guangdong

address: F2, Building 11, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics Center

country: China

institute: Beijing Genomics Institute

description:
Gathered from mountain creek.
SRX212984

data_processing:
Illumina Pipeline v1.3
Remove low quality reads
Getting rid of reads with 5' primer contaminants
Getting rid of reads without 3' primer
Getting rid of reads without the insert tag
Getting rid of reads with poly A
Getting rid of reads shorter than 18nt

organism: Dugesia japonica

source_name: cross cut,head part

growth_protocol: Planarian growth environment: indoor aquaculture, 20C or so,seven day’s starvation.

extract_protocol:
Three days’ after cut, following purification, total RNA samples were immediately preserved in ethanol and stored at -80C until further use.
Libraries were constructed with the Illumina Small RNA Kit version 1.5.

value: somatic cells

tag: developmental stage

value: asexual stage

tag: rna subtype

value: small RNA


title: DJ3

description:
Gathered from mountain creek.
SRX212985

source_name: cross cut,tail part


title: HCT15 [MBD MethylMagnet]

description: Sample 1

value: MethylMagnet


title: DU145 [MBD MethylMagnet]

description: Sample 2


title: DJ1

description:
Gathered from mountain creek.
SRX212983

source_name: whole body


title: HCT15 [MBD MethylCollector Ultra]

description: Sample 7


title: PC3 [MBD MethylMiner]

description: Sample 15

value: PC3 (purchased from ATCC)


title: Lizard liver Bio-CAP

city: Oxford

first: David

last: Sims

address: Parks Road

department: MRC Functional Genomics Unit

country: United Kingdom

institute: University of Oxford

data_processing:
Bio-CAP reads were aligned to the appropriate reference genomes using Bowtie version 0.12.7 allowing a maximum of two mismatches in the entire read, and retaining only uniquely mapping reads
PCR duplicates were removed uisng Picard MarkDuplicates version 1.79
Peaks were called using MACS version 14 vs input
Peaks closer than 200bp apart were merged
Peaks from biological replicates were merged and only peaks found in both replicated were retained
Genome_build: anoCar2,danRer7,xenTro3,mm9,hg19, galGal3,ornAna1
Supplementary_files_format_and_content: bed files of replicated Bio-CAP peaks

organism: Anolis carolinensis

source_name: liver

extract_protocol:
Samples were obtained either as purified genomic DNA, as fresh-frozen samples or were dissected in-house and fresh-frozen. Samples were subjected to manual homogenisation followed by DNA purification by phenol chloroform extraction or using the QIAGEN 100/G genomic tip kit.  For each individual Bio-CAP experiment, 25 μl of NeutrAvidin Agarose Resin (Thermo Scientific, 29200) was washed with BC100 buffer and then incubated with 50 μl of 0.5 μg/μl biotinylated hKDM2b-CxxC protein diluted in BC100 buffer for 1 hour at 4°C. The conjugated resin/CxxC protein was then washed with CAP100 buffer (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 100 mM NaCl). Genomic DNA was sonicated to an average size of 150-250 bp using a Diagenode Bioruptor. Sonicated DNA was then diluted in CAP100 buffer to a concentration of 16 μg/ml and a 100 μl Input sample was retained. For each Bio-CAP experiment, 500 μl of diluted sonicated DNA, corresponding to approximately 8 μg of DNA, was added to the conjugated CxxC resin. The DNA and resin were incubated at 4°C for 1 hour with gentle mixing. The resin was then collected by centrifugation at 1500 x g for 3 minutes at 4°C, and the unbound flowthrough (FT) material was removed. The resin and any associated DNA was washed twice with 1 ml of CAP100 buffer, before the first elution was performed by adding 50 μl of CAP300 (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 300 mM NaCl) to the resin and incubating at room temperature for 10 minutes. Following centrifugation a 50 μl elution fraction was carefully collected. The elution process was repeated using another 50 μl of CAP300 and the 300 mM elution fractions were pooled (giving a total volume of 100 μl). Subsequent elutions were performed in the same way using buffers with 500 mM, 700 mM and 1 M NaCl sequentially. Each 100 μl elution fraction, together with 100 μl of both the Input and FT samples, was purified using a PCR purification column (Qiagen) and DNA was eluted in a volume of 50 μl.  The 700 mM and 1 M fractions were pooled for sequencing. Bio-CAP material was quantified using the High Sensitivity Qubit system (Invitrogen) and the fragmentation profile was assessed using a DNA HS Agilent 2200 TapeStation chip. Bio-CAP material was then prepared for Solexa sequencing using the NEBNextTM DNA Sample Prep Master Mix Set 1, according to manufacturer's specifications. All Bio-CAP experiments were performed in duplicate with matched input controls.
Next generation sequencing was performed using two Illumina sequencing platforms: Genome Analyser IIx and HiSeq Systems yielding 51bp single-end reads. Sequencing was carried out according to the manufacturer’s instructions.

value: liver


title: HCT15 [MBD MethylMiner]

description: Sample 13


title: Lizard testes INPUT

source_name: testis

value: testis


title: HCT15 [RRBS]

description: Sample 16

value: RRBS


title: PC3 [MBD MethylMagnet]

description: Sample 3


title: Platypus testes INPUT

organism: Ornithorhynchus anatinus


title: Platypus testes Bio-CAP


title: Platypus liver Bio-CAP


title: Mouse liver Bio-CAP

tag: genetic background

value: Female C57Bl/6 and Male CBA/ca


title: Frog embryonic stage 11-12 Bio-CAP

organism: Xenopus tropicalis

source_name: stage 11-12 embryo

value: stage 11-12 embryo


title: H3122_input

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

description: Input

data_processing:
Bowtie alignment (H1819, H2087, H3122_2, H3122_FOXA1_ab23738) or GenePAST alignment (H3122_input and H3122_NKX2-1_BL4000)
read counts normalization in 100kb window size
Peak calling (MACS 1.4.0)
Genome_build: hg18
Supplementary_files_format_and_content: bed

extract_protocol: Crosslinked with 1% formaldehyde, washed with PBS, lysed in lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), sonicated with Covaris E210 to shear DNA to 200-1500bp. After immunoprecipitation or without immunoprecipitation for input, beads were washed, RNase A and Proteinase K treated and reverse crosslinked in elution buffer (1% SDS, 0.1M NaHCO3). DNAs were column purified and subjected to standard Illumina library construction.


title: H3122_NKX2-1_BL4000

description: IP

value: NKX2-1 [Bethyl Laboratories, BL4000]


title: Frog testes INPUT


title: Frog testes Bio-CAP


title: DJ4

description:
Gathered from mountain creek.
SRX212986

source_name: cliver cut,left part


title: DJ5

description:
Gathered from mountain creek.
SRX212987

source_name: cliver cut,right part


title: RNA-Seq H1 neural stem cells

city: Cambridge

middle: R

last: Kelley

state: MA

address: 7 Divinity Ave.

institute: Harvard University

data_processing:
Mapped reads against Hg19 using TopHat 1.1
Estimated gene abundance using Cufflinks 2.0
Genome_build: Hg19
Supplementary_files_format_and_content: Cufflinks .fpkm_tracking

extract_protocol: RNA was extracted from in-house cultured cell lines using TRIzol (Invitrogen) following the manufacturer instructions. After extraction a DNAse treatment was applied using Turbo DNAse (Ambion) and a second RNA extraction with TRIzol was performed. The standard mRNA-seq library preparations was done using the “Illumina mRNA-Seq Sample Prep Kit” (Part #RS-100-0801). Briefly, poly A+ RNA is purified from 100ng of total RNA with oligo-dT beads. Purified mRNA or RiboMinus RNA (200 ng) is then fragmented with divalent cations under elevated temperature. First strand cDNA synthesis is performed with random hexamers and reverse transcriptase. Second strand cDNA synthesis is performed using RNAseH and DNA Pol II. Following cDNA synthesis, double stranded products are end repaired, a single “A” base is added, and then the Illumina PE adaptors are ligated onto the cDNA products. For this study ligation products were purified using gel electrophoresis.  The target size range for these libraries was ~350-400 bp on the gel.  Following gel purification the adapter ligated cDNA is then amplified with 12-14 cycles of PCR.


title: RNA-Seq foreskin fibroblast iPSCs

source_name: foreskin fibroblast iPSC

value: foreskin fibroblast iPSC


title: RRBS_STHdhQ7_rep2

first: Christopher

last: Ng

state: Massachusetts

address: 77 Massachusetts Ave.

institute: Massachusetts Institute of Technology

description: RRBS

data_processing:
Bismarkv0.7.3 was used in directional mode for read alignment and methylation calls within the short reads.  A seed length of 40 and seed mismatch of 1 was used.
For each biological replicate, methylation and non-methylation calls are summed for each cytosine in CpG context on original top (OT) and original bottom (OB) annotation (mm9) strands.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited bedGraph file contains columns: (1) chromosome, (2) start position, (3) stop position, (4) methylation fraction [0-1], (5) total counts, (6) methylation counts
Supplementary_files_format_and_content: *OB.bedGraph genomic strand: -
Supplementary_files_format_and_content: *OT.bedGraph genomic strand: +

growth_protocol: STHdhQ7 and STHdhQ111 cell lines were cultured according as described previously (Trettel et al, Hum Mol Genet, 2000). In order to stop cell division and mitigate cell cycle differences, the culture is maintained at 33oC and raised to 39oC for two days prior to each experiment.

extract_protocol:
Genomic DNA for methylation studies was isolated using DNeasy Blood & Tissue kit (Qiagen cat. 69504) according to manufacturer’s recommended protocol. Genomic DNA integrity was assessed by 1% agarose gel and concentration is determined by Qubit dsDNA BR Assay kit (Invitrogen cat.  Q32850).
Reduced representation bisulfite libraries were prepared from Proteinase K treated, MspI digested DNA following ligation with methylated standard adapters, size selection, bisulfite conversion, and amplification of the final libraries.

value: Embyronic E14 striatal derived

tag: genotype

tag: passages

value: less than 15


title: RRBS_STHdhQ111_rep1

description: RRBS


title: RNA-Seq H1 embryonic stem cells


title: MeDIP_STHdhQ7

description: MeDIP-seq

data_processing:
MeDIP-Seq reads were aligned to the reference mouse genome (mm9) using Bowtie (v0.12.7).
MACS (v1.4) was used to shift positive and negative strand reads and generate*.wig format files.
Genome_build: MGSCv37

extract_protocol:
5ug of genomic DNA was sheared using Covaris S2 and standard Illumina libraries were constructed. 500ng of DNA library was then immunoprecipitated and enriched for DNA fragments containing 5-methylcytosine using the MeDIP kit according to the manufacturer’s recommended protocol (Active Motif cat. 55009).
18 cycles of PCR were then carried out and libraries were size selected using a 2% TBE agarose gel from 200-300bp. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: medip antibody

value: 5mC (Active Motif, part 103532, lot 16511002)


title: RRBS_STHdhQ7_rep1

description: RRBS


title: MeDIP_STHdhQ111

description: MeDIP-seq


title: ChIP_STHdhQ111_JUND_reps1and2

description:
ChIP-seq
processed data file: ChIP_STHdhQ7_STHdhQ111_JUND_GPS_significant.txt

data_processing:
ChIP-Seq reads were aligned to the reference mouse genome (mm9) using Bowtie (v0.12.7).
The enrichment of genomic regions for protein binding was assessed relative to a set of control reads obtained by sequencing unenriched IgG bound DNA.
Binding events were identified using the GPS algorithm(v1.1) with a calculated alignable genome size of 2.107 Gbp, a standard expected ChIP-Seq read distribution, a multiple hypothesis corrected enrichment q-value cutoff of 1e-2, and an alpha value of 20.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab delimited file contains GPS output with the following columns: Location (the genome coordinate), IP binding strength (the number of IP reads associated with the event), Control binding strength (the number of control reads in corresponding region), Fold enrichment (IP/Control), -log10(Q-value), -log10(P-value), IPvsEMP [KL divergence from the empirical read distribution (log10(KL))], IPvsCTR [KL divergence from the read density in the corresponding control region (log10(KL))]

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: chip antibody

value: Jund (Santa Cruz, sc-74x, lot B0111)


title: ChIP_STHdhQ7_JUND_reps1and2


title: Mouse testes INPUT


title: ChIP_STHdhQ111_FRA2_reps1and2

description:
ChIP-seq
processed data file: ChIP_STHdhQ7_STHdhQ111_FRA2_GPS_significant.txt

value: Fra-2 (Santa Cruz, sc-604x, lot I0210)


title: Lizard testes Bio-CAP


title: Bmp4f/+ lower molar

city: Cincinnati

first: Shihai

last: Jia

state: Ohio

address: 3333 Burnet Ave

department: Division of Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to the mm9 whole genome using Bowtie v0.12.7.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009 (PMID 19528076). Implanted in TopHat 1.4.1 using parameters:tophat -G mm9.gtf -o tophat -p 4 -r 0 mm9 reads.fastq. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values (abundance measurements) for each Sample.

source_name: molar mesenchyme, lower molar, control

extract_protocol: E13.5 mouse embryo heads were frozen in OCT in liquid nitrogen. The molar mesenchyme was microdissected by LCM after frozen section. Microdissected tissues were frozen at -80℃. Total RNA was extracted by using the RNeasy Micro Kit from Qiagen. cDNA was made by the NuGEN Ovation RNA-Seq v2 Assay. After obtaining the cDNAs, the sequencing libraries were generated by using illumina Nextera DNA Sample Prep kit.

value: mixed background

tag: age

value: embryonic day 13.5

value: molar mesenchyme (lower molar)


title: Bmp4f/+ upper molar

source_name: molar mesenchyme, upper molar, control

value: molar mesenchyme (upper molar)


title: Bmp4f/f;Wnt1Cre upper molar

source_name: molar mesenchyme, upper molar, Bmp4 mutant


title: Big lung tumor tissue with Dnmt3a intact

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph-format containing the genomic methylation ratios of the respective sample

source_name: lung tumors

growth_protocol: K-ras LSL-G12D mice were crossed with the Dnmt3a conditional KO mice. After adenoviral Cre recombinase –mediated recombination, mice were generated with lung cells that carried the K-ras G12D mutation and were homozygous (KO) and WT at the Dnmt3a locus. Tumors were flash-frozen in liquid nitrogen and stored at -80°C.

extract_protocol: 5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

treatment_protocol: adenoviral Cre recombinase was delivered to mice of 6-12 weeks old via intratracheal or intranosal approach

tag: genotype/variation

value: WTB


title: Small lung tumor tissue with Dnmt3a intact

value: WTS


title: Bmp4f/f;Wnt1Cre lower molar

source_name: molar mesenchyme, lower molar, Bmp4 mutant


title: RNA-Seq lung fibroblast iPSCs

source_name: lung fibroblast iPSC

tag: cell type

value: lung fibroblast iPSC


title: Small lung tumor tissue with Dnmt3a knocked out

value: KOS


title: Canton S, w1118 (Rep1)

city: St Lucia

first: Marina

last: Naval Sanchez

address: Carmody Road 306

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

data_processing:
Read mapping was performed using theBioscope Whole Transcriptome (WT) Pipeline (Applied Biosystems)
Gene counts were calculated by HTSeq package vesrion 0.53, function htseq-count.
Genome_build: dm3
Supplementary_files_format_and_content: Gene counts. Number of reads per gene from htseq-count.

source_name: wild-type

extract_protocol: Total RNA from 150 late pupal fly heads (73-90 hours APF) was extracted using Trizol reagent. Ribosomal RNA was removed using the RiboMinusTM Eukaryote Kit for RNA-seq (Invitrogen). SOLiD™ Whole Transcriptome Analysis.

value: late pupae heads

value: 73-90 hours APF


title: Big lung tumor tissue with Dnmt3a knocked out

value: KOB


title: TDP43 LOF (dTDP-43Δ23/Δ142) (Rep2)

source_name: TDP43 LOF


title: Healthy lung tissue

source_name: healthy lung tissue

value: Control


title: TDP43 GOF (act5c>dTDP-43) (Rep2)

source_name: TDP43 GOF


title: Mouse esc Bio-CAP

source_name: embryonic stem cell V6.5

tag: cell line

value: embryonic stem cell V6.5


title: TDP43 LOF (dTDP-43Δ142/Df(2R)106) (Rep1)


title: RRBS_STHdhQ111_rep2

description: RRBS

value: Embyronic E14 striatal derived

value: less than 15


title: Mouse testes Bio-CAP

value: testis

value: Female C57Bl/6 and Male CBA/ca


title: TDP43 LOF (dTDP-43Δ23/Δ142) (Rep1)


title: ChIP_STHdhQ7_SOX2_reps1and2

description:
ChIP-seq
processed data file: ChIP_STHdhQ7_SOX2_GPS_significant.txt


title: ChIP_STHdhQ111_IgG_reps1and2

description:
ChIP-seq
processed data file: none

value: IgG (Santa Cruz, sc-2027, lot J2909)


title: TDP43 GOF (act5c>dTDP-43) (Rep1)


title: RNA_STHdhQ111_reps1-3

description: messenger RNA

data_processing:
Paired-end reads were aligned to the mouse (RefSeq, mm9) transcriptome using the spliced junction discovery tool, TopHat(v1.4.0), and short-read alignment tool, Bowtie(v0.12.7).
Differential expression across the biological triplicates in each condition were called using the Cufflinks algorithm(v2.0.2) with bias and multi-read correction options.  Reads mapping to rRNA and mitochondrial transcripts were masked.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited file contains cuffdiff output with columns: (1) tested id, (2) gene, (3) locus , (4) sample 1, (5) sample 2, (6) test status, (7) FPKM of the gene in sample 1, (8) FPKM of the gene in sample 2, (9) log2(FPKM_2/FPKM_1), (10) test statistic, (11) p-value, (12) q-value, (13) significant (yes or no). See http://cufflinks.cbcb.umd.edu/manual.html for more details.

extract_protocol:
mRNA-Seq was performed following the Illumina mRNA Sequencing Sample Preparation Guide (Ilumina, Cat # RS-930-1001). mRNA was isolated from DNA-free total RNA using an Illumina-supplied mRNA Purification Kit. Oligo(dT) conjugated beads were used to pull-down poly-(A)-containing mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols. mRNA was fragmented using divalent cations under elevated temperature. First and second strand cDNA was then synthesized using random primers, end-repaired, adenylated and ligated with paired-end adapters (Illumina, catalog no. PE102-1004). The cDNA library was size-fractionated via gel electrophoresis. After staining of the gel in SYBR green, a narrow slice (~2 mm, +/- 25bp) of the cDNA lane centered at the 300bp marker was cut. cDNA from the gel slice was extracted using the Qiagen PCR mini elute kit (Qiagen, catalog no. 28006). The sample was then amplified by PCR and purified over a Qiagen PCR mini elute kit (Qiagen, catalog no. 28006).


title: ChIP_STHdhQ7_FRA2_reps1and2

value: Fra-2 (Santa Cruz, sc-604x, lot I0210)


title: H3122_FOXA1_ab23738

description: IP

tag: antibody


title: H3122_NKX2-1_BL4000_2

description: IP

value: NKX2-1 [Bethyl Laboratories, BL4000]


title: H1819_input

description: Input


title: H2087_input

description: Input


title: H3122_input_2

description: Input


title: RNA_STHdhQ7_reps1-3

description: messenger RNA


title: TDP43 LOF (dTDP-43Δ142/Df(2R)106) (Rep2)


title: H1819_NKX2-1_BL4000

description: IP


title: Zebrafish 24hr post fertilisation Bio-CAP

organism: Danio rerio

source_name: 24 hours post-fertilisation

value: 24 hours post-fertilisation embryo

value: KCL WT, AB and tubingen


title: Canton S, w1118 (Rep2)


title: Chicken liver Bio-CAP

organism: Gallus gallus

source_name: liver

value: liver


title: Zebrafish liver Bio-CAP


title: H2087_NKX2-1_BL4000

description: IP


title: Zebrafish testes Bio-CAP

source_name: testis


title: Human liver Bio-CAP


title: Zebrafish testes INPUT


title: Chicken testes Bio-CAP


title: Chicken testes INPUT


title: Frog liver Bio-CAP


title: Human testes INPUT


title: WT 2010

status: Public on Jan 21 2013

city: San Francisco

first: Phillip

middle: Anthony

last: Dumesic

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: University of California, San Francisco

data_processing:
Unique sequence tags were counted from the original sequence reads with and without applying a quality filter. Tags were truncated at the 3′ linker sequence (TCGTAT) prior to alignments.
Tags were then mapped to the loci encoding rRNA and tRNA genes, allowing up to one mismatch and randomly sampling multiple alignments where applicable.
Tags which did not align to the rRNA or tRNA were then repeatedly aligned against the full genome, allowing only perfect matches and randomly sampling multiple alignments where necessary, by adding a random suffix added as the readname for the observed count of each tag, after quality filtering
Mapping was performed using Bowtie version 0.12.7
Genome_build: Sequence and feature files for C. neoformans var. grubii H99 were obtained from the Broad Institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: tagcount file contains the sequence of each tag, the number of times it is seen, whether it includes the linker sequence (0=no, 1=yes), and the number of times it is seen when a quality filter is applied to the reads
Supplementary_files_format_and_content: BED file lists genomic regions giving rise to siRNAs in wild-type cells, identified as follows: The genome of C. neoformans was parsed into non-overlapping 100 bp windows.  Windows with high levels of siRNA reads (22-23 nt, beginning with a U) were selected by applying a read density cutoff of ≥10 siRNA reads/window. Adjacent windows passing the cutoff were merged

organism: Cryptococcus neoformans

source_name: Yeast

growth_protocol: 100ml cultures of cells in YPAD were grown at 30˚C to an OD600 of 1.0, at which point cells were isolated and snap frozen

extract_protocol:
Total RNA was isolated using TRIzol reagent.
cDNA libraries were prepared from small RNAs as described (Grimson et al. 2008 Nature 455: 1193-1197)

value: CM18 (wild-type)

tag: media

value: YPAD

tag: cell density


title: Myc ChIP in interphase

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

description: chromatin IP against Myc in interphase Kc cells

data_processing:
Sequences are aligned against the built-in index for D. melanogaster in bowtie-0.12.7 with most default parameters but -m which is set to 1
Tag density files for normalized abundance measurement are created by MACS (1.4.0) with default parameter
buid: dm3

source_name: Kc cells in interphase

growth_protocol: Kc cells are growed in CCM3 medium in 25 degree incubater

extract_protocol: 5~10e7 cells were used for chromatin preparations, sonicated 12 cycles (10s on / 30s off) on a BRANSON SONIFIER 250 with output control set at 1.5. ChIP is performed with Myc antibody (sc-28208). Libraries were prepared with the Illumina TruSeq DNA Sample Preparation Kit

value: Kc cells in interphase


title: ChIP_STHdhQ7_IgG_reps1and2

description:
ChIP-seq
processed data file: none


title: BEAF_interphase_ChIPSeq

city: Atlanta

first: Elizabeth

last: Sung

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

description:
Chromatin IP against BEAF in interphase
antibody from rabbit (animal 17368)  produced in our lab

data_processing: Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.

source_name: Kc cells

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched with glycine and cells were blocked with 5% BSA and incubated overnight at 4°C with antibodies against H3S10ph.  Cells were washed and incubated overnight with Alexa Fluor 488 anti-rabbit.  The next day, cells were washed and stained with propidium iodide, and then sorted into interphase and mitotic populations.  After sorting, nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4°C with protein A sepharose beads and then incubated overnight with antibody at 4°C.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4°C.  After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

value: BEAF

value: Kc167 Drosophila Embryonic

tag: cell cycle phase

value: Interphase


title: SuHw_mitosis_ChIPSeq

description:
Chromatin IP against Su(Hw) in mitosis
antibody from rabbit (animal 406)  produced in our lab

value: Su(Hw)

value: Mitosis


title: dCTCF_mitosis_ChIPSeq

description:
Chromatin IP against dCTCF in mitosis
antibody from a mixture of guinea pig and rat (rats 67 and 68, guinea pigs 2097 and 2098) produced in our lab

value: dCTCF


title: BEAF_mitosis_ChIPSeq

description:
Chromatin IP against BEAF in mitosis
antibody from rabbit (animal 17368)  produced in our lab


title: CP190_mitosis_ChIPSeq

description:
Chromatin IP against CP190 in mitosis
antibody from rabbit produced in our lab


title: Myc ChIP in mitosis

description: chromatin IP against Myc in mitotic Kc cells

source_name: Kc cells in mitosis

value: Kc cells in mitosis


title: CP190_interphase_ChIPSeq

description:
Chromatin IP against CP190 in interphase
antibody from rabbit produced in our lab


title: H3K4me3_OPC_ChIPseq_Sample 12

status: Public on Jan 20 2013

city: Chengdu

first: Yang

last: Yu

state: Si Chuan

address: Ren Min Nan road

institute: Si Chuan University

data_processing:
ChIP-seq reads were aligned to the rn4 genome assembly
peaks were called using MACS version 1.4.0 with default settings.
peaks were further filtered using following criteria to define a more stringent protein-DNA interactome: 1) the p-value cutoff was set to <10-9; 2) an enrichment of 5 fold; 3) tag number > 20
Genome_build: rn4
Supplementary_files_format_and_content: bed files were generated using MACS 1.4.0

organism: Rattus norvegicus

source_name: oligodendrocyte precursor cells

growth_protocol: Primary rat iOLs were isolated from cortices of pups at P2 using a differential detachment procedure as previously described (Chen et al., 2007). Isolated rat iOLs were grown in the iOL Growth Medium (Sato medium supplemented mitogens 10 ng/ml PDGF-AA and 20 ng/ml bFGF).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIP-seq libraries were prepared using 5500 SOLiD Fragment Library Core Kit (PN 4464412) as recommended by the manufacturer.

treatment_protocol: iOLs are differentiated in Oligodendrocyte Differentiation Medium (Sato medium supplemented with 15 nM thyroid hormone T3 and 10 ng/ml ciliary neurotrophic factor).

tag: strain

value: Sprague-Dawley

value: Primary OPCs

tag: treatment

value: mitogen treatment

value: wild type

value: H3K4me3 (Abcam, ab1012)


title: H3K27Ac_iOL_ChIPseq_Sample 10

source_name: immature oligodendrocyte cells

value: primary iOLs

value: T3 treatment

value: H3K27Ac (Cell Signaling, 4354s)


title: H3K9me3_mOL_ChIPseq_Sample 17

source_name: mature oligodendrocyte cells

value: primary mOLs

value: H3K9me3 (Abcam, ab8896)


title: H3K4me3_mOL_ChIPseq_Sample 14


title: H3K27Ac_OPC_ChIPseq_Sample 9


title: H3K9me3_iOL_ChIPseq_Sample 16


title: H3K9me3_OPC_ChIPseq_Sample 15


title: Olig2_mOL_ChIPseq_Sample 8

value: Olig2 (Millipore, Ab9610)


title: Human testes Bio-CAP

tag: tissue

value: testis


title: H3K27Ac_mOL_ChIPseq_Sample 11


title: cKO_SC

description: RNA-seq

data_processing:
RNA-seq reads were aligned using Tophat.
Differential expressed genes were determined using Cufflink
Genome_build: mm9
Supplementary_files_format_and_content: cuffdiff output file

source_name: spinal cord

extract_protocol:
Spinal cords of mice with corresponding genotype were removed and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: post natal day 14

value: spinal cord


title: H3K4me3_iOL_ChIPseq_Sample 13


title: Brg1_iOL_ChIPseq_Sample 4

value: Brg1 (gift of J.Wu)


title: RNAPII_iOL_ChIPSeq_Sample 2

value: RNA polymerase II (Covance, CAT# MMS-126R)


title: Brg1_mOL_ChIPseq_Sample 5


title: RNAPII_OPC_ChIPSeq_Sample 1


title: Brg1_OPC_ChIPseq_Sample 3


title: dCTCF_interphase_ChIPSeq

description:
Chromatin IP against dCTCF in interphase
antibody from a mixture of guinea pig and rat (rats 67 and 68, guinea pigs 2097 and 2098) produced in our lab

value: dCTCF

value: Kc167 Drosophila Embryonic

value: Interphase


title: nGFP_input

status: Public on Jan 18 2013

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

data_processing:
For the ChIP-seq of PRDM14, Reads were summed in 10 bp bins along the chromosome for ChIP and WCE, respectively. The read number of each bin was normalized with the total number of aligned reads for each chromosome. Scanning the genome with a 300 bp (30 bin) sliding window, a one-sided Wilcoxon rank-sum test was performed to estimate the enrichment p-value for each window. The fold enrichment (ChIP/WCE) for each window was also calculated. To call peaks, we picked up the windows which satisfied the criteria of a fold enrichment > 3.0 and p-value < 1e-4 as candidates for binding sites (Langmead et al., 2009). To further eliminate uncertain sites, we removed the regions with low ChIP reads using either of two criteria: 1) The average number of ChIP reads per region/the average number of ChIP reads in the genome < 3.0; 2) The maximum read intensity in ChIP bins was less than 50. We derived the consensus sequence motif by using MEME (Hu et al., 2011).
Genome_build: mm9

source_name: ES cells

growth_protocol: ES cells were passaged in ESC maintenance medium [GMEM containing 2 mM L-glutamine (cat#11710-035; Invitrogen) with 1 × MEM non-essential amino acids (cat#11140-050; Invitrogen), 1 mM sodium pyruvate (cat#11360-070; Invitrogen), 100 M -mercaptoethanol (cat#21985-023; Invitrogen), 1 × 103 units/ml LIF (cat#ESG1107; Chemicon), and 20% FBS (Stem Cell Science)].

extract_protocol:
ESCs at 70–80% confluency (approximately 2×107 cells on 15 cm dish) were crosslinked with 1% formaldehyde for 5 min at RT and rinsed twice with 10 ml of cold PBS after quenching with 125mM glycine. The fixed cells were harvested by using a silicon scraper, collected by centrifugation at 700 g for 5 min at 4 ○C, resuspended in 5 ml of cold LB1 (20 mM Tris, 10 mM NaCl, 2.5 mM MgCl2, 0.2% NP-40, 1 mM PMSF, pH7.5) and pelleted by centrifugation at 1350 g for 5 min after the rotation for 10 min at 4 ○C. The pellet was resuspended in 5 ml of LB2 (20 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1 mM PMSF, pH8.0) and rotated for 10 min at 4 ○C. The nuclei were pelleted by centrifugation at 1350 g for 5 min at 4 ○C and lysed in 2 ml of LB3 (20 mM Tris, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritoneX-100, 0.1% sodium deoxycholate, 0.1% SDS, CompleteTM EDTA-free). The lysed nuclei were sonicated using the following conditions: Branson Sonifier 250D with standard tip; 15% output; 10 cycles (12sec ON, centrifugation at 13,200 g for 2 min at 4 ○C).
Protein-DNA complexes were immunoprecipitated for overnight at 4 ○C using 10 μg of antibodies bound to 250 μl of Dynabeads Protein G (Invitrogen). Immunoprecipitates were washed five times with 1 ml of RIRA buffer (50 mM HEPES-KOH, 0.5 M LiCl, 1 mM EDTA, 0.5% Na-Deoxycholate, 1% NP-40, pH 7.4), and once with 250 μl of TE50 (50 mM Tris, 10 mM EDTA, pH8.0). Beads were resuspended with 200 μl of EB (1% SDS, TE50). The complexes were eluted at 65 ○C for 20 min. The crosslinks for both the immunoprecipitated and input DNA fragments were reversed by incubating at 65 ○C for at least 6 hrs. After RNase A and Proteinase K digestion, the DNA is purified by phenol/chloroform extraction and EtOH precipitation with 30 μg glycogen and dissolved with TE.
DNA from whole cell extracts (WCE) and ChIP fractions was further sheared to an average size of approximately 150 bp by ultrasonication (Covaris, Woburn, MA), end-repaired, ligated to sequencing adapters and amplified according to the manufacturer’s instructions (Applied Biosystems SOLiD Library Preparation Protocol).
For the ChIP of PRDM14 using AGP14 ESC-like cells, gel-purified amplified DNA of between 100 and 150 bp was sequenced on Life Technologies SOLiD 4 platforms to generate single-end 50-bp reads. For SUZ12 and histone H3K27me3, amplified DNA of between 200 and 350 bp, purified using an Agencourt AMPureXP Kit, was sequenced on a Life Technologies SOLiD 5500xl platform to generate single-end 50 bp reads.

value: Prdm14-/-, rescued by EGFP

value: Mouse embryonic stem cells (mESCs)


title: AGP14_input

value: Prdm14-/-, rescued by AVI-EGFP-Prdm14 (AGP14)


title: Prdm14KO_input


title: Olig2_OPC_ChIPseq_Sample 6

value: Sprague-Dawley

value: Primary OPCs

value: mitogen treatment

value: wild type


title: Ctrl_SC

description: RNA-seq