title: K80.6-KO

data_processing:
alignment: Sequence reads were mapped to the mus musculus reference genome (mm9) via TopHat v1.2.0. Only uniquely mapping reads were taken into account.
counts: HTSeq v0.5.3p3 was used to count the number of genes for annotated genes. HTSeq was used in the “union” mode, with gene annotations from Ensembl release 62, grouping exons together based on gene_name (i.e., MGI symbols for protein-coding genes).
differential expression: normalization of gene expression levels and differential gene expression between WT and KO was calculated with DESeq v1.2.2.
Genome Build:
K80.6-KO-CAGATC.counts.txt: mm9

value: KO


title: K79.4-KO

status: Public on Dec 07 2012

type: SRA

city: Leuven

first: Bram

last: Van de Sande

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KU Leuven

library_source: transcriptomic

data_processing:
alignment: Sequence reads were mapped to the mus musculus reference genome (mm9) via TopHat v1.2.0. Only uniquely mapping reads were taken into account.
counts: HTSeq v0.5.3p3 was used to count the number of genes for annotated genes. HTSeq was used in the “union” mode, with gene annotations from Ensembl release 62, grouping exons together based on gene_name (i.e., MGI symbols for protein-coding genes).
differential expression: normalization of gene expression levels and differential gene expression between WT and KO was calculated with DESeq v1.2.2.
Genome Build:
K79.4-KO-CGATGT.counts.txt: mm9

molecule: total RNA

organism: Mus musculus

source_name: Nkx2-1-iCre targeted eGFP+ cells

extract_protocol: Trizol followed by RNeasy micro. RNA seq library is prepared for analysis according to the Illumina TruSeq protocol (www.illumina.com). Briefly, 100 ng of Total RNA is purified using poly-T oligo-attached magnetic beads to end up with poly-A containing mRNA. The Poly-A tailed mRNA is fragmented and cDNA is synthesized using SuperScript II. cDNA fragments is end repaired, purified with AMPure XP beads, A-tailed using Klenow exo-enzyme in the presence of dATP. Illumina provided paired end adapters with index are ligated to the A-tailed cDNA fragments and purified using AMPure XP beads. The resulting adapter-modified cDNA fragments are enriched by PCR using Phusion polymerase as follow: 30 s at 98°C, 15 cycles of (10 s at 98°C, 30 s at 60°C, 30 s at 72°C), 5 min at 72°C. PCR products are purified using AMPure XP beads and eluted in 30 µl of resuspension buffer. One microliter is loaded on an Agilent Technologies 2100 Bioanalyzer using a DNA 1000 assay to determine the library concentration and to check for quality. Cluster generation was performed according to the Illumina TruSeq SR Cluster kit v2 (cBot) Reagents Preparation Guide (www.illumina.com). Briefly, 6 RNA-seq libraries were pooled together to get a stock of 10 nM. One microliter of the 10 nM stock was denaturated with NaOH, diluted to 6.5 pM and hybridized onto the flowcell. The hybridized products are sequentially amplified, linearized and end-blocked according to the Illumina Single Read Multiplex Sequencing user guide. After hybridization of the sequencing primer, sequencing-by-synthesis was performed using the HiSeq 2000 with a 36-cycle protocol. The sequenced fragments were denaturated with NaOH using the HiSeq 2000 and the index-primer was hybridized onto the fragments. The index was sequenced with a 7-cycle protocol.

treatment_protocol: FACsorting

tag: strain

value: Swiss

tag: genotype/variation

tag: developmental stage

tag: tissue

value: telencephalon

tag: method

value: FACsorted cells


title: K79.5-WT

data_processing:
alignment: Sequence reads were mapped to the mus musculus reference genome (mm9) via TopHat v1.2.0. Only uniquely mapping reads were taken into account.
counts: HTSeq v0.5.3p3 was used to count the number of genes for annotated genes. HTSeq was used in the “union” mode, with gene annotations from Ensembl release 62, grouping exons together based on gene_name (i.e., MGI symbols for protein-coding genes).
differential expression: normalization of gene expression levels and differential gene expression between WT and KO was calculated with DESeq v1.2.2.
Genome Build:
K79.5-WT-TGACCA.counts.txt: mm9

value: WT


title: Small RNA from TRBP-/+ mouse tail fibroblast

city: Worcester

first: Ryuya

last: Fukunaga

state: Ma

address: 364 Plantation st.

department: BMP

country: USA

institute: Umass Medical School

description:
MTFTRBP+Un
Small RNA

data_processing:
The Illumina fastq files generated from the sequencing machine were processed by the following steps:
(1) (Required for libraries with barcodes) Using an in-house C++ script, fastq files were split into 3 or 4 fastq files based on the first 4 nucleotides of each sequence. Sequences whose first 4 nucleotides did not match any barcodes were discarded.
(2) Inserts from each fastq file were retrieved by identifying the first appearance of the first six nucleotides of the 3' adaptor in each sequence. Sequences with 'N' were discarded. Quality strings were ignored.
(3) Same insert sequences were pooled together, and their total number of being sequenced are indicated in the second column of the processed file.
Genome_build: mm9
Supplementary_files_format_and_content: Sequences + number of reads. Barcode and adapter sequences are removed, and the same reads are pooled together.

source_name: mouse tail fibroblast, TRBP-/+

extract_protocol: Total RNA was isolated from 0-10 day female fly heads or 3-5 day ovaries using mirVana (Ambion, Austin, TX, USA). For mouse cells, total RNA was isolated using Trizol (Ambion, Austin, TX, USA). The RNA was quantified by absorbance at 260 nm. 18-30 nt RNAs was selected from 100 micrograms total RNA by running a 15% denaturing urea-polyacrylamide gel (National Diagnostics, Atlanta, GA, USA). For fly samples, 2S rRNA was depleted by hybridization using a complementary, immobilized DNA oligonucleotide (5'-biotin-TCA ATG TCG ATA CAA CCC TCA ACC ATA TGT AGT CCA AGC A-3'). Briefly, for each library, 400 µl MyOne Streptavidin C1 Dynabeads (Invitrogen) were washed twice in 0.5× SSC (1× SSC: 150 mM sodium chloride, 15 mM sodium citrate, pH 7.0) at 4°C, then re-suspended in 400 µl 0.5× SSC. The beads were then loaded with 200 pmole DNA oligonucleotide at 4°C for 30 min, washed once in 0.5× SSC, re-suspended in 1 ml 0.5× SSC, and then warmed to 65°C for 5 min. Size-selected RNA (50 µg) was incubated at 80°C for 5 min, and then added to the pre-warmed beads and incubated at 50°C for 1 h. The beads were then removed by magnetic capture and the supernatant mixed with 3 volumes of ethanol, 0.3 M (f.c.) sodium acetate, pH 5.2, and 1 µl (20 µg/µl) glycogen (Roche, Indianapolis, IN, USA). 100 pmole of 3' pre-adenylated adapter (5'-rAppTCG TAT GCC GTC TTC TGC TTG T/ddC/-3') was ligated to small RNAs using Rnl2_1-249 (New England Biolabs) at 4 °C for overnight in 20 microliters in 50 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 10 mM DTT, 60 mg/ml BSA, and 10% (v/v) DMSO. 3' ligated product was purified from a 15% denaturing urea-polyacrylamide gel (National Diagnostics), and then ligated to 100 pmole of 5' RNA adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3' for non-barcoded library and 5'-GUU CAG AGU UCU ACA GUC CGA CGA UCNNNN-3' for barcoded library, NNNN=CGTC, TAGC, ATCC, or GCAC) using T4 RNA ligase (Ambion, Austin, TX, USA) at 4 °C for overnight in 20 microliters in 50 mM Tris-HCl, pH 7.8, 10 mM MgCl2, 10 mM DTT, 1 mM ATP, and 10% DMSO. The ligated product was purified from a 10% denaturing urea-polyacrylamide gel (National Diagnostics). Half the ligated product was used to synthesize cDNA using Superscript III (Invitrogen) and the reverse transcription primer (5'-CAA GCA GAA GAC GGC ATA CGA-3'), and half was used as a minus RT control. The small RNA library was amplified using forward (5'-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3') and reverse (5'-CAA GCA GAA GAC GGC ATA CGA-3') primers, and then purified from a NuSieve GTG agarose gel (Lonza, Basel, Switzerland). Purified libraries were sequenced using an Illumina Genome Analyzer II (Illumina, San Diego, CA, USA).

value: TRBP-/+

value: mouse tail fibroblasts


title: K77.6-KO

data_processing:
alignment: Sequence reads were mapped to the mus musculus reference genome (mm9) via TopHat v1.2.0. Only uniquely mapping reads were taken into account.
counts: HTSeq v0.5.3p3 was used to count the number of genes for annotated genes. HTSeq was used in the “union” mode, with gene annotations from Ensembl release 62, grouping exons together based on gene_name (i.e., MGI symbols for protein-coding genes).
differential expression: normalization of gene expression levels and differential gene expression between WT and KO was calculated with DESeq v1.2.2.
Genome Build:
K77.6-KO-GCCAAT.counts.txt: mm9


title: K77.5-WT

data_processing:
alignment: Sequence reads were mapped to the mus musculus reference genome (mm9) via TopHat v1.2.0. Only uniquely mapping reads were taken into account.
counts: HTSeq v0.5.3p3 was used to count the number of genes for annotated genes. HTSeq was used in the “union” mode, with gene annotations from Ensembl release 62, grouping exons together based on gene_name (i.e., MGI symbols for protein-coding genes).
differential expression: normalization of gene expression levels and differential gene expression between WT and KO was calculated with DESeq v1.2.2.
Genome Build:
K77.5-WT-ACAGTG.counts.txt: mm9


title: CMLPh-003T

city: Monza

first: Roberta

last: Spinelli

state: MB

address: Via Cadore 48

department: Department of Health Science

country: Italy

institute: University of Milano Bicocca

description: GA pipeline version 1.5

data_processing:
Image processing and basecall were performed using the Illumina Real Time Analysis Software RTA v1.9.35. Qseq files were deindexed and converted in the Sanger-FastQ file format using in-house scripts.
FastQ sequences were aligned to the human genome database (NCBI36/hg18) by using TopHat 1 vs 1.2.0 using default parameters and the gene and splice junctions models supplied by the Human Ensembl GTF annotation file vs54 (Homo_Sapiens.NCBI36.54.GTF) downloaded from the Ensembl FTP server (ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/).
The quantitative gene expression profile was estimated by SAMMate vs.2.6.1 by using the Human Ensembl GTF annotation file vs54 and the default parameters
To focus on the gene expression profile of known coding transcripts, a dataset of 20,907 protein-coding Ensembl Genes was selected from the whole transcriptome matrix of FPKM expression values for 36,655 unique Ensembl Gene obtained by SAMMate
A splice junction map for SETBP1-mutated and non-mutated cases was inferred by TopHat
Genome_build: Human genome database (NCBI36/hg18)
Supplementary_files_format_and_content: Tab-delimited text files include the chromosome, the Gene Name, the Ensembl Gene ID, Biotype, sum exon length of the gene, the gene reads counts and the normalized FPKM measurements of each protein_coding biotype for each sample generated by SAMMate using the Human GTF annotation file (vs54) and default parameters

organism: Homo sapiens

source_name: Atypical Chronic Myeloid Leukemia cells

extract_protocol:
Total RNA was extracted with TRIzol® (Invitrogen, Life technology, Grand Island, NY, USA) using the standard protocol.
2ug total RNA was processed according to Illumina TruSeqTM RNA Sample Preparation Kit (FC-122-1001) protocol modified for the time of fragmentation: mRNA was shared for 1 minute at 94°C and, after the ligation of the adapters, fragments of 400-500bp were selected on 2% agarose gel

treatment_protocol: Leukemic cells were obtained by separation on a Ficoll-Paque Plus gradient (GE Healthcare, UK). The phenotype was evaluated by FACS analysis and myeloid cells (CD33, CD13, CD117) were >80% of total cells.

tag: genotype

value: SETBP1 G870S -/+


title: sob-F3-5_SOLEXA_5

status: Public on Dec 06 2012

first: Scot

last: Wolfe

state: MA

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

description:
molecule: plasmid DNA
Sample 118

library_source: other

data_processing:
The extracted sequences from the Illumina data were submitted to MEME for analysis. The parameters used as follows: Motif width was set at 5 to 15, the distribution of motif set as zoops, while allowing sites on + or - DNA strands. All other parameters were at the default settings. Aligned sequences were subsequently extracted from the MEME results and output in fasta format.
Supplementary_files_format_and_content: fasta and contains aligned extracted binding site sequences along with 'sequence rank.number'  For example, '457.1'  represent the corresponding unique sequence is ranked 457th and is 1 in number.
Supplementary_files_format_and_content: In the file name,  e.g. CG3407_SOLEXA_2.5.fa,   CG3407 refers to Gene name, SOLEXA denotes the sequencing method and 2.5 is the inhibitor (3-AT) concentration used in the Bacterial One-Hybrid selection.

molecule: other

organism: synthetic construct

source_name: synthetic library

growth_protocol: refer to Enuameh MS et al. 2012 [PMID 22689783]

extract_protocol:
Following each selection, all of the cells were scraped off the plate. The randomized portion of the prey vector containing the selected transcription factor binding sites were extracted and amplified using PCR.
The PCR products from different experiments were digested with different restriction enzymes in the first step of uniquely encoding sequences from different experiments. The restriction enzyme fragments were then barcoded, pooled and sequenced using a Illumina Genome Analyzer IIx or Illumina HiSeq 2000 machine as indicated in Gupta et al. (2011). Nucleic Acids Res. 39(1): 381–392. A more detailed description of the selection  conditions employed for each zinc finger cluster is given in the methods section of this publication as well as the supplemental material of Noyes et al. (2008). Cell. 133(7):1277-1289.

tag: library

value: ZFP library

tag: library selection

value: bacterial one-hybrid (B1H) selected


title: sob-F1-3_SOLEXA_5

description:
molecule: plasmid DNA
Sample 117

treatment_protocol: refer to Enuameh MS et al. 2012 [PMID 22689783]


title: Sens2-F4-6_SOLEXA_5

description:
molecule: plasmid DNA
Sample 115


title: Sqz-F1-3_SOLEXA_5

description:
molecule: plasmid DNA
Sample 119


title: pho-F1-3_SOLEXA_5

description:
molecule: plasmid DNA
Sample 112


title: sna-F2-4_SOLEXA_5

description:
molecule: plasmid DNA
Sample 116


title: Rn-F2-4_SOLEXA_5

description:
molecule: plasmid DNA
Sample 113


title: Small RNA from female fly head of wIR: loqsKO; loqs-PB, loqs-PD/TM3

description:
wIRloqsKOPBDUn
Small RNA

data_processing:
The Illumina fastq files generated from the sequencing machine were processed by the following steps:
(1) (Required for libraries with barcodes) Using an in-house C++ script, fastq files were split into 3 or 4 fastq files based on the first 4 nucleotides of each sequence. Sequences whose first 4 nucleotides did not match any barcodes were discarded.
(2) Inserts from each fastq file were retrieved by identifying the first appearance of the first six nucleotides of the 3' adaptor in each sequence. Sequences with 'N' were discarded. Quality strings were ignored.
(3) Same insert sequences were pooled together, and their total number of being sequenced are indicated in the second column of the processed file.
Genome_build: dm3
Supplementary_files_format_and_content: Sequences + number of reads. Barcode and adapter sequences are removed, and the same reads are pooled together.

organism: Drosophila melanogaster

source_name: female fly head, wIR: loqsKO; loqs-PB, loqs-PD/TM3

extract_protocol: Total RNA was isolated from 0-10 day female fly heads or 3-5 day ovaries using mirVana (Ambion, Austin, TX, USA). For MEFs, total RNA was isolated using Trizol (Ambion, Austin, TX, USA). The RNA was quantified by absorbance at 260 nm. 18-30 nt RNAs was selected from 100 micrograms total RNA by running a 15% denaturing urea-polyacrylamide gel (National Diagnostics, Atlanta, GA, USA). For fly samples, 2S rRNA was depleted by hybridization using a complementary, immobilized DNA oligonucleotide (5'-biotin-TCA ATG TCG ATA CAA CCC TCA ACC ATA TGT AGT CCA AGC A-3'). Briefly, for each library, 400 µl MyOne Streptavidin C1 Dynabeads (Invitrogen) were washed twice in 0.5× SSC (1× SSC: 150 mM sodium chloride, 15 mM sodium citrate, pH 7.0) at 4°C, then re-suspended in 400 µl 0.5× SSC. The beads were then loaded with 200 pmole DNA oligonucleotide at 4°C for 30 min, washed once in 0.5× SSC, re-suspended in 1 ml 0.5× SSC, and then warmed to 65°C for 5 min. Size-selected RNA (50 µg) was incubated at 80°C for 5 min, and then added to the pre-warmed beads and incubated at 50°C for 1 h. The beads were then removed by magnetic capture and the supernatant mixed with 3 volumes of ethanol, 0.3 M (f.c.) sodium acetate, pH 5.2, and 1 µl (20 µg/µl) glycogen (Roche, Indianapolis, IN, USA). 100 pmole of 3' pre-adenylated adapter (5'-rAppTCG TAT GCC GTC TTC TGC TTG T/ddC/-3') was ligated to small RNAs using Rnl2_1-249 (New England Biolabs) at 4 °C for overnight in 20 microliters in 50 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 10 mM DTT, 60 mg/ml BSA, and 10% (v/v) DMSO. 3' ligated product was purified from a 15% denaturing urea-polyacrylamide gel (National Diagnostics), and then ligated to 100 pmole of 5' RNA adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3' for non-barcoded library and 5'-GUU CAG AGU UCU ACA GUC CGA CGA UCNNNN-3' for barcoded library, NNNN=CGTC, TAGC, ATCC, or GCAC) using T4 RNA ligase (Ambion, Austin, TX, USA) at 4 °C for overnight in 20 microliters in 50 mM Tris-HCl, pH 7.8, 10 mM MgCl2, 10 mM DTT, 1 mM ATP, and 10% DMSO. The ligated product was purified from a 10% denaturing urea-polyacrylamide gel (National Diagnostics). Half the ligated product was used to synthesize cDNA using Superscript III (Invitrogen) and the reverse transcription primer (5'-CAA GCA GAA GAC GGC ATA CGA-3'), and half was used as a minus RT control. The small RNA library was amplified using forward (5'-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3') and reverse (5'-CAA GCA GAA GAC GGC ATA CGA-3') primers, and then purified from a NuSieve GTG agarose gel (Lonza, Basel, Switzerland). Purified libraries were sequenced using an Illumina Genome Analyzer II (Illumina, San Diego, CA, USA).

value: wIR:loqsKO; loqs-PB, loqs-PD/TM3

tag: gender

value: female

value: head


title: l(3)neo38-F2-4_SOLEXA_5

description:
molecule: plasmid DNA
Sample 108


title: Sens-F1-3_SOLEXA_5

description:
molecule: plasmid DNA
Sample 114


title: Gl_SOLEXA_F3-5

description:
molecule: plasmid DNA
Sample 104


title: lmd-F3-5_SOLEXA_5

description:
molecule: plasmid DNA
Sample 109


title: CG31670-F1-3_SOLEXA_5

description:
molecule: plasmid DNA
Sample 101


title: CG14962-F2-4_SOLEXA_5

description:
molecule: plasmid DNA
Sample 100


title: CG10267_SOLEXA_F3-5

description:
molecule: plasmid DNA
Sample 99


title: CG10267-F1-3_SOLEXA_5

description:
molecule: plasmid DNA
Sample 98


title: Small RNA from female fly head of wIR: loqsKO; loqs-PA/TM3

description:
wIRloqsKOPAUn
Small RNA

source_name: female fly head, wIR: loqsKO; loqs-PA/TM3

value: wIR:loqsKO; loqs-PA/TM3


title: her_SOLEXA_F2-4

description:
molecule: plasmid DNA
Sample 105


title: CG8319-F5-7_SOLEXA_5

description:
molecule: plasmid DNA
Sample 97


title: CG7928-F5-7_SOLEXA_5

description:
molecule: plasmid DNA
Sample 96


title: vfl_SOLEXA_5

description:
molecule: plasmid DNA
Sample 88


title: wor_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 89


title: 16.5 WT1

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped to mm9 using TopHat 1.3.2/bowtie 0.12.7.0 with default settings
FPKM values and fold changes were calculated using cufflinks/cuffdiff 1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: Series supplementary files include FPKM values and fold changes for 3 comparisons

source_name: E16.5 skin

extract_protocol: Skin was removed and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: skin

tag: age

value: embryonic day 16.5

value: wild type


title: sug_SOLEXA_5

description:
molecule: plasmid DNA
Sample 85


title: sr_SOLEXA_5

description:
molecule: plasmid DNA
Sample 84


title: sqz_SOLEXA_5

description:
molecule: plasmid DNA
Sample 83


title: Sp1_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 82


title: sna_SOLEXA_5

description:
molecule: plasmid DNA
Sample 80


title: phol_SOLEXA_5

description:
molecule: plasmid DNA
Sample 73


title: sens_SOLEXA_5

description:
molecule: plasmid DNA
Sample 77


title: rn_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 74


title: sob_SOLEXA_5

description:
molecule: plasmid DNA
Sample 81


title: pho_SOLEXA_5

description:
molecule: plasmid DNA
Sample 72


title: pad_SOLEXA_5

description:
molecule: plasmid DNA
Sample 69


title: luna_SOLEXA_5

description:
molecule: plasmid DNA
Sample 66


title: ovo_SOLEXA_5

description:
molecule: plasmid DNA
Sample 68


title: lola-PW_SOLEXA_5

description:
molecule: plasmid DNA
Sample 64


title: lola-PT_SOLEXA_5

description:
molecule: plasmid DNA
Sample 62


title: lola-PU_SOLEXA_5

description:
molecule: plasmid DNA
Sample 63


title: lola-PQ_SOLEXA_5

description:
molecule: plasmid DNA
Sample 61


title: Klu_SOLEXA_F2-4

description:
molecule: plasmid DNA
Sample 107


title: pad-F2-4_SOLEXA_5

description:
molecule: plasmid DNA
Sample 111


title: lola-PG_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 56


title: lola-PO_SOLEXA_5

description:
molecule: plasmid DNA
Sample 59


title: lola-PD_SOLEXA_5

description:
molecule: plasmid DNA
Sample 54


title: KD5day-plusDox3 (GAGTACG)

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

description: Total RNA was isolated from GemKD cells differentiated in N2B27 media for 5 days with or without addition of 500 ng Dox for Gem knockdown from day 3. These samples were used for RNA-seq analysis (Illumina HiSeq2000 platform) by the Genome Technology Access Center (GTAC) at Washington University School of Medicine in St. Louis. Three independent experiments were conducted to generate Geminin knockdown (plus Dox) samples and these were compared to the no-Dox control.

data_processing:
Sequence alignment to the mm9 genome was performed by GTAC using TopHat with the following settings: a. min anchor=5; m. splice mismatches=1; i. min intron length=10; I. max intron length=500000; g. max # of multi hits=100 (solexa 1.3 quals)
Transcript abundance was determined by GTAC using Cufflinks with option I=500000.
Genes that were differentially expressed between the experimental (plus Dox) and control (no Dox) samples were defined using Cuffdiff (Trapnell et al., Nature Protocols 7: 562-78) (http://cufflinks.cbcb.umd.edu/manual.html).
Transcripts were considered as differentially expressed upon Gem knockdown if data met statistical significance cutoffs in Cuffdiff (sufficient sequence alignments were obtained for analysis and transcript had significant change in FPKM value (normalized transcript abundance; fragments per kb of exon per million fragments mapped) between the no Dox and plus Dox sample pairs) in at least two of the three independent experiments.
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output: Matrix files from comparisons of experimental versus control samples, which were used to define differentially expressed genes.

source_name: neural progenitors derived from mouse embryonic stem cells, Geminin knockdown

growth_protocol: The A2lox mouse ES cell line and clonal derivatives were routinely propagated on feeder cells (mouse embryonic fibroblast cells; Chemicon) in DMEM (Invitrogen) supplemented with 15% FCS (HyClone), 1 mM sodium pyruvate, 1 mM non-essential amino acids, 1 mM L-glutamine (Invitrogen), 10−4 M 2-mercaptoethanol (Sigma), and 10exp3 units per milliliter of leukemia inhibitory factor (ESGRO; Chemicon). Monolayer neural differentiation of ES cells was done as previously described (Yellajoshyula et al., PNAS 108(8), pg. 329). Briefly, ES cells cultured on feeder cells were dissociated and plated at 1 × 10exp5/cm2 for 1 day on 0.1% gelatin-coated tissue culture dishes. After 24 h, cells were plated onto 0.1% gelatin-coated tissue culture dishes at low density (1 × 10exp4 cells/cm2) in N2B27 medium and cultured for 5 days.

extract_protocol: RNA was isolated from the cells using the Trizol Plus RNA purification system (Invitrogen). Library construction was conducted by the Genome Technology Access Center (GTAC) at Washington University School of Medicine, according to standard protocols for Illumina HiSeq NextGen sequencing (http://gtac.wustl.edu/services/sequencing/library-preparation.php) . Four samples indexed with the indicated sequence tags were sequenced on a lane of the Illumina HiSeq.

treatment_protocol: ES cells enabling doxycycline-dependent Geminin knockdown (described previously, Yellajoshyula et al., PNAS 108(8), pg. 329) were treated with 500ng doxycycline from day 3 to day 5 of neuronal differentiation in N2B27 medium. RNA samples were collected for library construction and sequencing on day 5.

tag: es cell line

tag: cell type

value: embryonic stem cell-derived neural precursors

tag: treatment

value: plus Dox

tag: library label

value: GAGTACG


title: lola-PK_SOLEXA_5

description:
molecule: plasmid DNA
Sample 51


title: lola-PJ_SOLEXA_5

description:
molecule: plasmid DNA
Sample 50


title: KD5day-plusDox2 (CTCAATG)

institute: Washington University School of Medicine

value: CTCAATG


title: lola-PI_SOLEXA_5

description:
molecule: plasmid DNA
Sample 49


title: KD5day-plusDox1 (ACAGATA)

value: ACAGATA


title: scrt_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 76


title: l(3)neo38_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 47


title: lmd_SOLEXA_5

description:
molecule: plasmid DNA
Sample 48


title: klu_SOLEXA_5

description:
molecule: plasmid DNA
Sample 45


title: input_2

status: Public on Dec 11 2012

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: service: Deep Sequencing Facility, D-BSSE, Basel, Switzerland

library_source: genomic

data_processing:
Sequenced reads were mapped to dm3 whole genome using bowtie version 0.12.7 with parameters  -m 1 (single reads) and --trim3 65 -X 1500 (paired end reads)
calculation of genomic coverage vectors for each sample using a 150 bp read extension for single read samples
arcsine transformation of coverages
averaging of replicate samples
subtraction of common background (input)
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph files of the mean genomic coverage

molecule: genomic DNA

source_name: Input

extract_protocol: As performed by sequencing service

tag: ip antibody

value: none (input)

tag: shearing technologie

value: Bioruptor

tag: chromatin size (bp)


title: jim_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 43


title: ken_SOLEXA_5

description:
molecule: plasmid DNA
Sample 44


title: esg-F3-5_SOLEXA_5

description:
molecule: plasmid DNA
Sample 38


title: gl_SOLEXA_5

description:
molecule: plasmid DNA
Sample 40


title: KD5day-noDox1 (GTATTTG)

data_processing:
Sequence alignment to the mm9 genome was performed by GTAC using TopHat with the following settings: a. min anchor=5; m. splice mismatches=1; i. min intron length=10; I. max intron length=500000; g. max # of multi hits=100 (solexa 1.3 quals)
Transcript abundance was determined by GTAC using Cufflinks with option I=500000.
Genes that were differentially expressed between the experimental (plus Dox) and control (no Dox) samples were defined using Cuffdiff (Trapnell et al., Nature Protocols 7: 562-78) (http://cufflinks.cbcb.umd.edu/manual.html).
Transcripts were considered as differentially expressed upon Gem knockdown if data met statistical significance cutoffs in Cuffdiff (sufficient sequence alignments were obtained for analysis and transcript had significant change in FPKM value (normalized transcript abundance; fragments per kb of exon per million fragments mapped) between the no Dox and plus Dox sample pairs) in at least two of the three independent experiments.
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output: Matrix files from comparisons of experimental versus control samples, which were used to define differentially expressed genes. The files are linked to the experimental sample records.

source_name: neural progenitors derived from mouse embryonic stem cells, control

value: no Dox

value: GTATTTG


title: fru-PI_SOLEXA_5

description:
molecule: plasmid DNA
Sample 39

value: ZFP library

value: bacterial one-hybrid (B1H) selected


title: hb_SOLEXA_5

description:
molecule: plasmid DNA
Sample 41


title: her_SOLEXA_10

description:
molecule: plasmid DNA
Sample 42


title: CG32830_SOLEXA_5

description:
molecule: plasmid DNA
Sample 32


title: CG14962_SOLEXA_5

description:
molecule: plasmid DNA
Sample 28


title: CG12605_SOLEXA_5

description:
molecule: plasmid DNA
Sample 27


title: CG17181_SOLEXA_5

description:
molecule: plasmid DNA
Sample 29


title: CG31670_SOLEXA_5

description:
molecule: plasmid DNA
Sample 30


title: CG12029_SOLEXA_5

description:
molecule: plasmid DNA
Sample 24


title: D19B-F10-12_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 35


title: CG9895_SOLEXA_5

description:
molecule: plasmid DNA
Sample 21


title: CG31782-F9-11_SOLEXA_5

description:
molecule: plasmid DNA
Sample 31


title: CG10267_SOLEXA_5

description:
molecule: plasmid DNA
Sample 22


title: disco_SOLEXA_5

description:
molecule: plasmid DNA
Sample 36


title: CG8319_SOLEXA_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 20


title: CG7928_SOLEXA_5

description:
molecule: plasmid DNA
Sample 19


title: XH low weight

city: Guangzhou

first: Xinzheng

last: Jia

state: Guangdong

address: Wushan Road

department: Animal Science

country: China

institute: South China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were first processed to filter out reads containing adapters, unknown or low quality bases and then were mapped to the chicken reference genome (ftp://ftp.ensembl.org/pub/release-63/fasta/gallus_gallus/dna/) by SOAPaligner v 2.21 (http://soap.genomics.org.cn/) with no more than 2 bp mismatches
Genome-wide methylation peak scanning was conducted using the MACS V 1.4.2 (http://liulab.dfci.harvard.edu/MACS/).The uniquely mapped data were retained for reads distribution analysis including the distribution in chicken chromosomes and the distribution in different components of the genome.
Genome_build: gallus_gallus.WASHUC2.63
Supplementary_files_format_and_content: Methylation peak files were conducted using the MACS V 1.4.2 (http://liulab.dfci.harvard.edu/MACS/).

organism: Gallus gallus

source_name: breast muscle

growth_protocol: WRR, a breed with fast growth rate, were obtained from Guangdong Wens Foodstuff Company Ltd, Guangdong, China. XH, a Chinese native breed with slow growth rate, were obtained from Zhicheng Avian Breeding Company Ltd, Guangdong, China. All broilers were reared in cages with a 24-h photoperiod for the first 2 d of age and then changed to a 16-h photoperiod. They were fed with free access to water and fed ad libitum with 16.5% CP and 2, 800 kcal of ME/kg. At 7 weeks of age, according to the body weight records, 3 female birds from each of the two-tail samples of WRR and XH were selected and then four groups including WRRh, WRRl, XHh, and XHl were generated. The BW values were 1,064.0 ± 11.1, 695.0 ± 24.4, 305.8 ± 23.3, and 207.6 ± 11.1 g in the WRRh, WRRl, XHh, and XHl group, respectively.

extract_protocol:
Genomic DNA was isolated using TaKaRa Universal Genomic DNA Extraction Kit Ver. 3.0 (DV811A) (TaKaRa, Osaka, Japan) according to the manufacturer’s protocol and then DNA quality was evaluated by agarose gel electrophoresis and spectrophotometer.
DNA from 3 birds within each group was mixed in equal amounts to generate a pooled sample using Quant-iT dsDNA HS Assay Kit (Invitrogen, Carlsbad, CA, USA). Subsequently, these four pooled samples were sonicated to produce DNA fragments ranging from 100-500 bp.After end repairing, phosphorylating and A-tailing with Paired-End DNA Sample Prep kit (Illumina, San Diego, CA, USA), DNA was ligated to an Illumina sequencing primer adaptor. Then the fragments were used for MeDIP enrichment using Magnetic Methylated DNA Immunoprecipitation kit (Diagenod, Liège, Belgium) following the manufacturer’s recommendation and the qualifying DNA was used for PCR amplification. Then bands between 220 and 320 bp were excised from the gel and purified with QIAquick Gel Extraction Kit (Qiagen, Valencia, CA, USA). Products were quantified with Quant-iTTM dsDNA HS Assay Kit (Invitrogen, Carlsbad, CA, USA) on an Agilent 2100 Analyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Breast muscle tissues of the 12 individuals were collected and stored at -80°C until DNA extraction.

tag: breed

value: Xinhua

tag: phenotype

value: low weight

value: breast muscle

value: 7 weeks


title: XH high weight

value: high weight


title: WRR low weight

value: Recessive White Rock


title: CG7368_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 18


title: CG5669_SOLEXA_5

description:
molecule: plasmid DNA
Sample 17


title: WRR high weight


title: CG2052_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 12


title: CG12236-PA_SOLEXA_5

description:
molecule: plasmid DNA
Sample 25


title: CG3407_SOLEXA_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 14


title: CG4854_SOLEXA_5

description:
molecule: plasmid DNA
Sample 16


title: br-PA_SOLEXA_5

description:
molecule: plasmid DNA
Sample 6


title: bteb2_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 9


title: br-PC_SOLEXA_10

description:
molecule: plasmid DNA
Sample 5


title: br-PL_SOLEXA_5

description:
molecule: plasmid DNA
Sample 8


title: Blimp-1_SOLEXA_5

description:
molecule: plasmid DNA
Sample 3


title: INPUT_ZT26

city: Lausanne

first: Nouria

last: Hernandez

state: Vaud

address: Dorigny

department: CIG

country: Switzerland

institute: UNIL

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT26.bedGraph: (NCBI37/mm9)

source_name: input

growth_protocol: C57/BL6 male, 12-14 week old (at time of sacrifice), mice were housed in a 12h Light/12h dark light regimen for 2 weeks with food and water available ad libitum during night and day.

extract_protocol: Chromatin from cell lysates was sonicated and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: They were then entrained with a 12h Light/12h dark light regimen with food access between ZT12 and ZT24 for 7 days (ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off).  At each ZT02 and, as a biological replicate, ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 5 ml of PBS through the spleen and immediately collected. Up to 100 mg of liver was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The rest of the livers was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation.

tag: strain

tag: tissue type

value: liver

tag: chip antibody

tag: chiip antibody manufacturer

tag: chip antibody catalog number

tag: chip antibody lot/batch


title: INPUT_ZT22

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT22.bedGraph: (NCBI37/mm9)


title: Pat190_MeDIP-seq

city: Berlin

first: Michal-Ruth

last: Schweiger

address: Ihnestr. 63-73

department: Vertebrate Genomics

institute: Max-Planck-Institut for Molecular Genetics

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat190_MeDIP-seq_sorted_filtered.bed.gz: GRCh37

source_name: prostate tumor biopsy

growth_protocol: Primary samples from 51 prostate cancer tissues were obtained after radical prostatectomies.

extract_protocol:
DNA preparation: For Laser Capture Microdissection (LCM, Zeiss, Germany) of epithelial cells, 16µm tissue sections were mounted on special LCM slides and briefly stained with hematoxilin and eosin to facilitate localization of epithelial cells. Epithelial cells were collected by LCM from 10 tissue sections each. DNA was isolated using the DNA mini kit (Qiagen) according to the manufacturer's instructions. From macrodissected samples the AllPrep DNA/RNA/Protein Mini Kit was used.
Methylation profiling by MeDIP-Seq: In brief, 2.5µg of genomic DNA were fragmented to 100 to 200bp using the Covaris S2 system and end repaired with End Repair mix (Enzymatics) followed by a purification step (Qiagen DNA purification kit). Barcoded sequencing adapters were ligated followed by nick translation with DNA polymerase I (NEB, 10U). For the enrichment step of the methylated DNA immunoprecipitation (MeDIP) 5µg of an anti-5-methyl cytosine antibody (Eurogentec) coupled to magnetic beads were used. Coupling was performed by incubation overnight in 1xPBS + 0.5% BSA. Sequencing libraries were generated prior to the enrichment and incubated with the beads for 4 hours in IP Buffer (10mM sodium phosphate buffer pH 7, 140mM NaCl, 0.25% Triton X100). Beads were washed three times with IP buffer and DNA was eluted in elution buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS) by incubation for 15min at 65°C. After two hours of incubation with proteinase K, the DNA was phenol/chloroform extracted and ammonium acetate/ethanol precipitated. Enrichment controls were performed with real time PCRs targeting methylated as well as unmethylated regions. SOLiD sequencing libraries were prepared following the SOLiD v3 fragment multiplex library preparation protocol (Life Technologies) with slight modifications. Following MeDIP enrichments libraries were amplified with multiplex library PCR primers 1 and 2, size-selected and quantified. Sequencing was performed on a SOLiD 3+ using barcode sequencing chemistry (5+35 bp) (Lifetech).
Barcoded sequencing libraries were prepared according to the SOLiD protocol , enriched with an anti-5methyl cytosine antibody (Eurogentec: Clone 33D3) and sequenced with the SOLiD fragment 35+5bp barcode sequencing technology (Lifetech).

tag: tumor stage

tag: gleason


title: Pat118_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat118_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: ab_SOLEXA_5

description:
molecule: plasmid DNA
Sample 1

tag: library

tag: library selection


title: INPUT_ZT14

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT14.bedGraph: (NCBI37/mm9)


title: INPUT_ZT18

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT18.bedGraph: (NCBI37/mm9)


title: Pat115_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat115_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat116_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat116_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: INPUT_ZT10

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT10.bedGraph: (NCBI37/mm9)


title: Pat117_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat117_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat113_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat113_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: INPUT_ZT06

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT06.bedGraph: (NCBI37/mm9)


title: INPUT_ZT02

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT02.bedGraph: (NCBI37/mm9)


title: CG3065-F1-5_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 13

data_processing:
The extracted sequences from the Illumina data were submitted to MEME for analysis. The parameters used as follows: Motif width was set at 5 to 15, the distribution of motif set as zoops, while allowing sites on + or - DNA strands. All other parameters were at the default settings. Aligned sequences were subsequently extracted from the MEME results and output in fasta format.
Supplementary_files_format_and_content: fasta and contains aligned extracted binding site sequences along with 'sequence rank.number'  For example, '457.1'  represent the corresponding unique sequence is ranked 457th and is 1 in number.
Supplementary_files_format_and_content: In the file name,  e.g. CG3407_SOLEXA_2.5.fa,   CG3407 refers to Gene name, SOLEXA denotes the sequencing method and 2.5 is the inhibitor (3-AT) concentration used in the Bacterial One-Hybrid selection.


title: H3K36me3_ZT26

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K36me3_ZT26.bedGraph: (NCBI37/mm9)

source_name: H3K36me3 IP

value: Abcam


title: H3K36me3_ZT22

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K36me3_ZT22.bedGraph: (NCBI37/mm9)


title: H3K36me3_ZT18

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K36me3_ZT18.bedGraph: (NCBI37/mm9)


title: Pat110_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat110_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat83_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat83_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat105_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat105_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: H3K36me3_ZT14

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K36me3_ZT14.bedGraph: (NCBI37/mm9)


title: H3K36me3_ZT10

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K36me3_ZT10.bedGraph: (NCBI37/mm9)


title: H3K36me3_ZT06

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K36me3_ZT06.bedGraph: (NCBI37/mm9)


title: Pat80_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat80_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: H3K36me3_ZT02

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K36me3_ZT02.bedGraph: (NCBI37/mm9)


title: Pat82_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat82_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: H3K4me3_ZT18

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K4me3_ZT18.bedGraph: (NCBI37/mm9)

source_name: H3K4me3 IP


title: Pat81_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat81_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat111_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat111_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat62_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat62_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: H3K4me3_ZT22

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K4me3_ZT22.bedGraph: (NCBI37/mm9)


title: H3K4me3_ZT02

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K4me3_ZT02.bedGraph: (NCBI37/mm9)


title: Pat64_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat64_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat57_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat57_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat59_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat59_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: H3K4me3_ZT26

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K4me3_ZT26.bedGraph: (NCBI37/mm9)


title: H3K4me3_ZT06

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K4me3_ZT06.bedGraph: (NCBI37/mm9)


title: Pat63_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat63_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat61_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat61_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: H3K4me3_ZT10

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K4me3_ZT10.bedGraph: (NCBI37/mm9)


title: Pat60_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat60_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: H3K4me3_ZT14

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K4me3_ZT14.bedGraph: (NCBI37/mm9)


title: Pat55_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat55_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Polr2b_ZT26

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT26.bedGraph: (NCBI37/mm9)

source_name: RPB2 IP

value: Santa Cruz Biotechnology


title: Pat53_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat53_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat51_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat51_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Polr2b_ZT18

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT18.bedGraph: (NCBI37/mm9)


title: Polr2b_ZT10

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT10.bedGraph: (NCBI37/mm9)


title: Polr2b_ZT14

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT14.bedGraph: (NCBI37/mm9)


title: Pat49_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat49_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Polr2b_ZT22

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT22.bedGraph: (NCBI37/mm9)


title: Polr2b_ZT06

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT06.bedGraph: (NCBI37/mm9)


title: Pat48_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat48_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Polr2b_ZT02

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT02.bedGraph: (NCBI37/mm9)


title: 5p_nhlh2_SOLEXA_5

description:
molecule: plasmid DNA
Sample 125

data_processing:
The extracted sequences from the Illumina data were submitted to MEME for analysis. The parameters used as follows: Motif width was set at 5 to 15, the distribution of motif set as zoops, while allowing sites on + or - DNA strands. All other parameters were at the default settings. Aligned sequences were subsequently extracted from the MEME results and output in fasta format.
Supplementary_files_format_and_content: fasta and contains aligned extracted binding site sequences along with 'sequence rank.number'  For example, '457.1'  represent the corresponding unique sequence is ranked 457th and is 1 in number.
Supplementary_files_format_and_content: In the file name,  e.g. CG3407_SOLEXA_2.5.fa,   CG3407 refers to Gene name, SOLEXA denotes the sequencing method and 2.5 is the inhibitor (3-AT) concentration used in the Bacterial One-Hybrid selection.


title: 5p_irs1b-like_SOLEXA_5

description:
molecule: plasmid DNA
Sample 124


title: Pat47_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat47_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat45_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat45_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: 5p_cpe_SOLEXA_5

description:
molecule: plasmid DNA
Sample 123


title: Pat54_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat54_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat44_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat44_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat42_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat42_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat43_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat43_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: 3p_nhlh2_SOLEXA_5

description:
molecule: plasmid DNA
Sample 122


title: lola-PQPJ_SOLEXA_5

description:
molecule: plasmid DNA
Sample 110


title: Pat41_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat41_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: ken-F1_CG4360-F2-3_SOLEXA_5

description:
molecule: plasmid DNA
Sample 106


title: Pat52_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat52_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: D19B-F1-2_CG4360-F3_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 103


title: Pat38_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat38_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat40_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat40_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat39_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat39_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: ci-F3-5_SOLEXA_5

description:
molecule: plasmid DNA
Sample 102


title: Pat37_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat37_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat36_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat36_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat35_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat35_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Br-PAPE_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 95


title: Br-PAPC_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 94


title: Blimp-1-F1_CG4360-F2-3_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 93


title: Pat34_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat34_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: BCl6-F5_CG4360-F2-3_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 92


title: 3p_irs1b-like_SOLEXA_5

description:
molecule: plasmid DNA
Sample 121


title: BCl6-F4-6_SOLEXA_5

description:
molecule: plasmid DNA
Sample 91


title: BCl6-F1-6_SOLEXA_5

description:
molecule: plasmid DNA
Sample 90


title: 3p_cpe_SOLEXA_5

description:
molecule: plasmid DNA
Sample 120


title: ttk-PF_SOLEXA_5

description:
molecule: plasmid DNA
Sample 87


title: Pat33_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat33_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat31_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat31_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat32_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat32_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: ttk-PA_SOLEXA_5

description:
molecule: plasmid DNA
Sample 86

data_processing:
The extracted sequences from the Illumina data were submitted to MEME for analysis. The parameters used as follows: Motif width was set at 5 to 15, the distribution of motif set as zoops, while allowing sites on + or - DNA strands. All other parameters were at the default settings. Aligned sequences were subsequently extracted from the MEME results and output in fasta format.
Supplementary_files_format_and_content: fasta and contains aligned extracted binding site sequences along with 'sequence rank.number'  For example, '457.1'  represent the corresponding unique sequence is ranked 457th and is 1 in number.
Supplementary_files_format_and_content: In the file name,  e.g. CG3407_SOLEXA_2.5.fa,   CG3407 refers to Gene name, SOLEXA denotes the sequencing method and 2.5 is the inhibitor (3-AT) concentration used in the Bacterial One-Hybrid selection.


title: Pat30_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat30_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: shn-F1-2_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 79


title: salr-F3-5_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 75


title: Pat28_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat28_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat27_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat27_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat26_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat26_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: peb-F5-7_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 71


title: Pat25_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat25_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat29_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat29_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: opa_SOLEXA_5

description:
molecule: plasmid DNA
Sample 67


title: Pat23_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat23_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: Pat21_MeDIP-seq

description: IP against methylated Cytosine

data_processing:
Bed files: Reads were aligned to HG19 using the Bioscope v1.0 pipeline from Lifetech with standard settings for 35mer reads. The aligned reads were elongated to 200bp in a strand-oriented manner. Redundant reads and reads with no CpGs in the elongated sequence were excluded.
Genome Build:
Pat21_MeDIP-seq_sorted_filtered.bed.gz: GRCh37


title: lola-PP_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 60


title: lola-PF_SOLEXA_5

description:
molecule: plasmid DNA
Sample 55


title: lola-PC_SOLEXA_5

description:
molecule: plasmid DNA
Sample 53


title: lola-PY_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 65


title: peb-F1-3_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 70


title: lola-PN_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 58


title: crol-F7-16_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 34


title: CG12236-PB_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 26


title: CG11071_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 23


title: sens2_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 78


title: Kr_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 46


title: br-PE_SOLEXA_5

description:
molecule: plasmid DNA
Sample 7


title: Cf2-PB_SOLEXA_5

description:
molecule: plasmid DNA
Sample 11


title: Aef1_SOLEXA_5

description:
molecule: plasmid DNA
Sample 2


title: ci_SOLEXA_5

description:
molecule: plasmid DNA
Sample 33


title: lola-PL_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 57


title: Genomic DNA of gastric cancer patient NGCII092 tumour_IlluminaGAII

status: Public on Dec 05 2012

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

institute: University of Cologne

description:
genomic DNA was fractionated using Roche Nebulizer in 400-600 bp fragments , and sequenced by 2x101bp.
Identification of SNVs, indels, and genomic structural variations

data_processing:
Paired-end Illumina reads were mapped to the reference human genome (NCBI Build 36) using ELAND (Illumina Inc.) and reads that failed pass-filter were removed from further analysis.
Sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite v0.31 and v4.0 (Applied Biosystems). Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described in the README file (linked as Supplementary file on Series record).
Processed data files linked below and on the Series record.

source_name: gastric adenocarcinoma of a patient without active H. pylori infection and microsatellite instability but with intestinal metaplasia

growth_protocol: primary tissue, no growth conditions

extract_protocol:
For Illumina short insert libraries, genomic DNA was randomly fractionated using Roche Nebulizer following manufacturer's instructions. Fractionated DNA was then end-repaired, A-tailed at 3'end, ligated with Illumina paired end adaptors, PCR amplified followed by gel-selection of a range of 400-600 bp fragments as templates, and sequenced by Illumina GA from both ends to obtain 76 bp and 101 bp reads, respectively, at each end.
For Solid long insert libraries, genomic DNA was hydrosheared, EcoP15I recognition sites were methylated and EcoP15I CAP adaptors were ligated to the ends of DNA fragments. The methylated DNA constructs were separated on agarose gel and 10 kb sized fragments were selected for ligation resulting in circularized products where 5' and 3' ends of the DNA fragments were connected by an internal biotinylated adaptor with two flanking non-methylated EcoP15I CAP adaptors. Constructs were digested by methylation sensitive EcoP15I to release 5' and 3' paired-end tag (PET) constructs. Sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by the Applied Biosystems SOLiD system.

treatment_protocol: no treatment

tag: tumor type

value: stage 1b, intestinal Lauren classification, moderately differentiated and of tubular subtype

tag: tissue

value: tumour


title: Genomic DNA of gastric cancer patient NGCII092 blood_IlluminaGAII

source_name: mononuclear blood cells

value: non affected tissue

value: blood


title: Genomic DNA of gastric cancer patient NGCII092 tumour_SOLiDv2

description:
genomic DNA hydrosheared in 11.4 kb fragments (std dev: 1011 bp), 2x25bp paired-end (mate pair) sequences
Identification of SNVs, indels, and genomic structural variations


title: Genomic DNA of gastric cancer patient NGCII082 tumour_SOLiDv2

description:
genomic DNA hydrosheared in 9.6 kb fragments (std dev: 876 bp below median; 612 bp above median), 2x25bp paired-end (mate pair) sequences
Identification of SNVs, indels, and genomic structural variations

source_name: gastric adenocarcinoma of a patient with active H. pylori infection, chronic gastritis, microsatellite instability

value: stage 3b, intestinal Lauren classification, moderately differentiated and of tubular subtype


title: Genomic DNA of gastric cancer patient NGCII082 blood_SOLiDv2

description:
genomic DNA hydrosheared in 10.3 kb fragments (std dev: 705 bp below median; 1050 bp above median), 2x25bp paired-end (mate pair) sequences
Identification of SNVs, indels, and genomic structural variations


title: Genomic DNA of gastric cancer patient NGCII082 tumour_IlluminaGAII


title: Senescent/shLuc p53

city: New York

first: Ozlem

last: Aksoy

state: NY

address: 415 East 68th Street

department: Watson School of Biological Sciences

institute: CSHL

description: P53 ChIP-seq in Ras-induced senescent cells

data_processing:
The Illumina  GA sequencing tags were mapped to the unmasked human  reference genome (NCBI version 36, hg18) using the program  Bowtie with the parameter setting ‘‘-t -q -a –best –strata -m 1.’’, duplicate reads were removed
ChIP-seq peak regions were determined using MACS (Zhang  et al. 2008) to find ChIP-enriched regions compared with the  input DNA control with default parameter settings and a significance  threshold (P<1e-5).
Supplementary_files_format_and_content: Bowtie mapped reads, duplicate reads removed
Supplementary_files_format_and_content: MACS called peaks with Mock as control

source_name: IMR90 Human Fetal Lung Fibroblast cell line

extract_protocol: The immunoprecipitated DNA was prepared for Illumina sequencing as described (Chicas et al. 2010).

treatment_protocol: IMR90 cells were infected with Ras vector and indicated hairpins. The cells were collected 7 days after puro selection. The ChIP experiments were done as previously described (Chicas et al. 2010).

value: p53 antibody (Cat number:sc-126 DO-1) from Santa Cruz (10 ug) [mouse monoclonal antibody, Lot:F0909]

tag: cell line

tag: cell type

value: Human Fetal Lung Fibroblast cell line


title: Growing p53

description: P53 ChIP-seq in growing cells


title: Senescent/shp53 p53

description: P53 ChIP-seq in Ras-induced senescent cells with P53 knockdown


title: lola-PA_SOLEXA_5

description:
molecule: plasmid DNA
Sample 52

source_name: synthetic library

value: ZFP library

value: bacterial one-hybrid (B1H) selected


title: Mock (IgG)

description: IgG ChIP-seq in growing cells

value: Anti-mouse IgG [Santa Cruz Biotechnology, Mouse monoclonal antibody, Catalog number:Sc-2025, Lot:C1111]


title: disco-r-F1-2_SOLEXA_5

description:
molecule: plasmid DNA
Sample 37


title: Non-tumor sample 9N

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

description: rRNA-depleted RNA

data_processing: High-throughput sequencing reads were mapped against human genome assembly (NCBI Build GRCh37). The reads with at most 2 mismatches and a maximum of 10 mappable locations were retained for calculation of gene expression. The gene expression level is measured by RPKM (number of exon reads mapped per kilobase per million mapped reads). The gene differential expression was evaluated using the t-test and Baggerley's test.

source_name: esophageal cell type

growth_protocol: Esophageal squamous cell carcinoma and adjacent non-tumorous tissues were obtained from patients immediately following resection, snapped-frozen in liquid nitrogen and stored in -80C freezer prior to RNA extraction.

extract_protocol: The total RNA samples were treated with DNA-free Kit (Ambion, Inc. TX, USA) to digest the DNA. Large 18S and 28S rRNAs were removed from 1ug total RNA with the RiboMinusTM Transcriptome Isolation kit (Human/Mouse) (Invitrogen, Carlsbad, CA, USA). The rRNA-depleted RNA was precipitated with Pellet Paint (Novagen Inc., Madison, Wis.), quality checked on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.). The rRNA-depleted RNA from 1 ug of total RNA was fragmented by incubation for 5 min at 94°C in 5 x Array Fragmentation Buffer (Ambion, Inc. TX, USA). The reaction was stop by chilling the tube on ice and precipitated with Pellet Paint. Double strand cDNA was synthesized with the SuperScript Double Stranded cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) using random hexamers according to the manufacturer's instructions. The reaction was cleaned up on a QiaQuick PCR column (Qiagen, Valencia, CA, USA). Ds cDNA fragments were repaired with DNA Terminator End Repair Kit End (Lucigen, Middleton, WI, USA) by incubation for 30 min at 30°C and then were cleaned up on a QiaQuick PCR column. The Klenow 3' to 5' exo- (NEB, Ipswich, MA) was used to add a single 'A' base to the 3'end of blunt phosphorylated DNA fragments by incubation for 30 min at 30°C. After clean-up on a QiaQuick PCR column, Illumina PE Adapter was ligated to the end of DNA fragments with the Quick Ligation Kit (NEB, Ipswich, MA) by incubation for 15 min at room temperature. The reaction was cleaned up on a QiaQuick PCR column. 180-200 bp fragments were excised from a 2% low range agarose gel. Fragments were enriched by 10 cycles using AccuPrime Pfx DNA Polymerase (Invitrogen, Carlsbad, CA, USA). PCR product was run on Novex 8% TBE polyacrylamide gel (Invitrogen, Carlsbad, CA, USA) and stained with SYBR Gold (Invitrogen, Carlsbad, CA, USA). The gel slice was cut off and cleaned up by QiaQuick Gel Extraction Kit (Qiagen, Valencia, CA, USA). The concentration of gel purified DNA fragments was measured by using a ND-1000 UV/Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA)

value: non-tumor


title: Genomic DNA of gastric cancer patient NGCII082 blood_IlluminaGAII


title: Non-tumor sample 6N

description: rRNA-depleted RNA


title: Non-tumor sample 5N

description: rRNA-depleted RNA


title: Cf2-PA_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 10


title: CG4360-F1-3_SOLEXA_2.5

description:
molecule: plasmid DNA
Sample 15


title: bowl_SOLEXA_5

description:
molecule: plasmid DNA
Sample 4


title: Non-tumor sample 4N

description: rRNA-depleted RNA


title: Tumor sample 8T

description: rRNA-depleted RNA

value: tumor


title: Genomic DNA of gastric cancer patient NGCII092 blood_SOLiDv2

description:
genomic DNA hydrosheared in 9.9 kb fragments (std dev: 491 bp below median; 429 bp above median), 2x25bp paired-end (mate pair) sequences
Identification of SNVs, indels, and genomic structural variations


title: Tumor sample 3T

description: rRNA-depleted RNA


title: Tumor sample 7T

description: rRNA-depleted RNA


title: Tumor sample 2T

description: rRNA-depleted RNA


title: Tumor sample 6T

description: rRNA-depleted RNA


title: Tumor sample 1T

description: rRNA-depleted RNA


title: mouse_ts_h3k4me1

status: Public on Dec 04 2012

city: Boulder

first: Edward

last: Chuong

address: 596 UCB

department: BioFrontiers

institute: University of Colorado Boulder

description: ChIP DNA

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 or rn4 using BWA 0.9.6 (-q 10 -I), and filtered using samtools view (-q 1) to remove multiply mapping reads.
Individual alignments were merged using samtools merge, then peaks were called using MACS v2.0.9 with default settings, using --broad setting for histone marks.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq bed files contain peaks called by MACS v2.0.9

source_name: Trophoblast stem cells

growth_protocol: Mouse TSCs were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004). Rat TSCs were cultured as previously (Asanoma et al, Developmental Biology 2011)

extract_protocol:
Cells were trypsinized for 4 minutes and prepared using the ChIP kit (Millipore). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II or HiSeq following the manufacturer's protocols.

value: Trophoblast stem cells


title: mouse_ts_input

description: Input chromatin


title: mouse_ts_3seq_rep1

description: mRNA

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 or rn4 using Bowtie 0.12.7 with the settings --best --strata -k 10 -S --chunkmbs 190
Using Unipeak v1.0, Bowtie alignments were filtered by posterior probability (sam_map.pl from Unipeak), and transcription peaks were called using default settings.
Peaks (chromosomal coordinates) were associated with Ensembl (e67) gene database for mouse and rat, and multiple peaks for each gene were pooled.
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain pooled gene x raw tag count

molecule: polyA RNA

extract_protocol:
mRNA was extracted directly from cell lysates using Dynabeads Oligo (dT)25 (Invitrogen).
500 ng of mRNA was then used to prepare 3’ RNA-Seq libraries as previously described (Beck et al, PLOS One 2010). Briefly, mRNA was heat sheared for 7 minutes to produce an average fragment size range of 300-500 bp, then used to generate cDNA libraries using a custom oligo dT primer containing Illumina-compatible adapter sequence. cDNA fragments were end-repaired and ligated to standard Illumina adapters. Size-selection was performed using E-gel SizeSelect agarose gels (Invitrogen), products were PCR amplified for 15 cycles, and purified using Ampure XP beads. Library quality was assessed using Bioanalyzer and Qubit, and sequenced on the Genome Analyzer IIx.


title: mouse_ts_h3k4me3

description: ChIP DNA


title: Non-tumor sample 8N

description: rRNA-depleted RNA


title: KAP1 ChIP: KAP1 KO TI

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

institute: EPFL

data_processing:
Raw reads were mapped to the mouse genome and transcriptome using Bowtie
Peaks were called using MACS
For histone modifications, enriched regions were defined using the ChIP-part suite
Genome_build: mm9

source_name: KAP1 ChIP: KAP1 KO TI

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma: G5154) with sodium pyruvate (used at 1mM, Sigma: S8636), MEM non-essential amino acids (used at 1x, Gibco: 11140-035), L-glutamine (used at 2mM, Gibco: 25030-024), 2-mercaptoethanol (used at 0.1mM, Sigma), ES cell tested FBS (Gibco: 16141-079) and leukaemia inhibitory factor (LIF, used at 1,000 units/ml, Chemicon: ESG1107). Cells were grown on 0.2% gelatin (Sigma: 48723-500G-F)-coated plates and split every two days.

extract_protocol: ES cell samples were washed 2x (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x24mm tubes (Covaris: 520056) and sonicated (Covaris settings: 20% duty cycle, intensity 5, 200cyles/ burst, 30 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine). Samples were also checked for the absence of single-stranded DNA by Exonuclease I treatment.

value: Embryonic stem cells (ES3)

tag: time-point

value: KO:4 days post 4-OHT inducible CRE

value: None (Total Input)