title: Normal male testis replicate B

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics

institute: BGI-SHENZHEN

description: processed data file: ZZ_male.Cdepth.txt

data_processing:
use the genome of Cynoglossus semilaevis as reference, BS-Seq reads were aligned onto the corresponding reference using soap v2.21 with default parameters except -m 175 -x 325 -s 40 -l 32 -v 4.
Short reads were aligned onto the reference genomes. To avoid the failure of reads mapping caused by additional mismatches resulting from C to T transition after bisulfite treatment, all Cs of the reference genome were in silico converted to Ts (T-genome) and all Gs were converted to As (A-genome) respectively. Moreover, the sequenced reads were prepared for alignment by replacing observed Cs on the forward read with Ts and observed Gs on the reverse reads with As. We used SOAP2 (Li et al. 2009b) to map the transformed reads to both the T- and A-genome, allowing up to 4 mismatches for 90 bp paired-end reads. Reads aligning to more than one position on the genome were discarded. Multiple reads mapping to the same position were regarded as PCR duplicates, and only one of them was kept. For mC detection, we retrieved the original sequence of the transformed reads compared it with the untrasformed reference genomes. Cytosines in BS-seq reads that matched to Cs on the reference were counted as potential mCs. Cytosines with a quality score < 20 were not considered. To determine the non-conversion rate of each library, 25 ng unmethylated Lambda DNA was mixed into DNA when library construction, following the previous method (Liu et al. 2012). The non-conversion rate of each library was calculated as the total number of sequenced Cs divided by the total sequencing depth for sites corresponding to Cs in the lambda genome. To distinguish true positives from false positives we used a model based on the binomial distribution B (n, p), with p equal to the non-conversion rate and n equal to the coverage depth of each potential mC. For example, given a potential mC position with k sequenced cytosines and total depth of n, we calculated the probability that all the k cytosines sequenced out of n trials were false positive, and then compared the probability of B (k, n, p) to 0.01 after adjusting the P-value by FDR (Benjamini et al. 2001). Only the mCs with adjusted P-values < 0.01 were considered true positives.
Genome_build: The reference genome of Cynoglossus semilaevis assembled from a female fish maintained in the facilities of the Key Laboratory of Sustainable Development of Marine Fisheries in Qingdao.
Supplementary_files_format_and_content: This file contains all the cytosines of the whole genome, one cytosine per line and further described in the  'readme_cdepth.txt' file avaiable on a Series records.

organism: Cynoglossus semilaevis

source_name: Normal male testis

extract_protocol: Up to 20 μg of total genomic DNA were isolated from each pooled sample. DNA was fragmented by sonication with a Covaris S2 system (Covaris, MA) to a mean size of approximately 250 bp, followed by end- repair, 3’-end addition of dA, and adapter ligation. Methylated adapters were used according to the manufacturer’s instructions (Illumina). The bisulfite conversion of sample DNA was carried out using a modified NH4HSO3-based protocol and amplified by 15 cycles of PCR. Paired-end sequencing was carried out using Illumina HiSeq 2000.

treatment_protocol: The bisulfite conversion of sample DNA was carried out using a modified NH4SO4-based protocol.

value: male

value: testis


title: C3-2

status: Public on Jan 23 2014

type: SRA

city: New York

first: Susan

middle: K.

last: Logan

state: New York

address: 522 1st Ave, Smilow Research Building, Rm # 1211

department: NYU Cancer Institute, Mol Pharm and Biochem

country: USA

institute: NYU School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
The 3' adaptor was removed from raw reads and reads with the length less than 10 were excluded to constitute the mappable reads.
The mappable reads were aligned against human genome using Bowtie v1.0.0.
Abundance estimation and differential expression analysis are done using Cufflinks v2.0.2.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: summary_isoforms_fpkm_tracking.xls: summary of read number and the isoform-level abundance of each sample
Supplementary_files_format_and_content: isoform_exp_diff.xls: pairwise comparison and statistical test results

molecule: total RNA

organism: Homo sapiens

source_name: prostate cancer cells

extract_protocol:
QIAGEN RNA Extraction Kit
Directional mRNA-Seq Sample Preparation

tag: sample type

value: Wnt inhibitor (C3) treated


title: C3-1


title: F1 pseudo-male testis replicate B

country: China

description: processed data file: ZW_male2.Cdepth.txt

library_source: genomic

molecule: genomic DNA

source_name: F1 pseudo-male testis

tag: generation

value: F1 offspring

tag: gender type

value: pseudo-male

tag: tissue


title: RARa binding in the RA-treatment group

city: Sacramento

first: Yuqi

last: He

state: California

address: Rm3400, Research III, UC Davis Medical Center, 4645 2nd Ave

institute: UC Davis Medical Center

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie
Peaks were called by using MACS
Genome_build: mm10
Supplementary_files_format_and_content: Peaks called by MACS were included in BED files

organism: Mus musculus

source_name: Liver

extract_protocol:
Grand in liquid nitrogen, then fixed, sonication, pull down by antibody
Illumina True-Seq Kit

treatment_protocol: Wild type C57/BL mice were treated with normal diet (control) or retinoic acid diet (RA) for 1 day by feeding

tag: strain

tag: gender

value: Male

tag: age

value: 3 Month

value: Liver


title: si-AR-1

value: AR knockdown


title: Normal male testis replicate A

description: processed data file: ZZ_male.Cdepth.txt


title: F1 pseudo-male testis replicate A


title: Parental pseudo-male testis replicate A

description: processed data file: ZW_male1.Cdepth.txt

source_name: Parental pseudo-male testis

value: parental


title: Parental ovary replicate B

description: processed data file: ZW_female1.Cdepth.txt

source_name: Parental normal female ovary

value: female

value: ovary


title: Parental pseudo-male testis replicate B


title: F1 ovary replicate B

description: processed data file: ZW_female2.Cdepth.txt

source_name: F1 normal female ovary


title: F1 ovary replicate A


title: Parental ovary replicate A


title: 36:11 Eed-/- DOX

city: Zurich

first: Valentina

last: Boeva

address: Universitatstrasse 6

department: Computer Science

country: Switzerland

institute: ETH Zurich

description: 36:11 Eed-/- DOX, JARID2

data_processing:
Alignment with Bowtie2, default parameters, N=1
For allele specific binding: filtering out alignment with the same edit distance to mm9 and Cast
Quality filtering: Phred alignment quality q>=20
Duplicate read filtering
BigWig file creation with HOMER, default parameters, fragLength=150
Genome_build: mm9
Genome_build: Mus Musculus Castaneus (Cast) for allele specific binding
Supplementary_files_format_and_content: BigWig, fragment density tracks

source_name: Embryonic stem cells

growth_protocol: TX1072 ES were grown in classical ESC medium (Chaumeil et al., 2006) + 2i - 2 inhibitors: MEF inhibitor -1μM PD0325901 and GSK3 inhibitor -3 μM Chir99021. TX1072 D4 DOX were differentiated towards the epiblast stem cell lineage in N2B27 medium with activin A (20 ng/ml) and FGF2 (12.5 ng/ml) in the presence of 1μg/ml of doxycycline for 4 days. 36:11 and 36:11 Eed-/- were grown in classical ESC medium (Chaumeil et al., 2006) on a feeder-layer; in the inducible samples, doxycycline (1μg/ml) was administrated for 3 days.

extract_protocol:
Lysates were clarified from sonicated nuclei and JARID2-DNA complexes were isolated with JARID2 antibody (Li et al., 2010)
ChIP-seq libraries were prepared according to Illumina protocol and sequenced using a HiSeq machine. Single-end sequencing was carried out to obtain about 50 million (M), 100bp long reads per sample. Read alignment with Bowtie2-2.1.0 (Langmead and Salzberg, 2012; Langmead et al., 2009) with standard parameters and one mismatch in the seed sequence and consecutive duplicate filtering resulted in at least 35M reads per sample. Only reads with mapping quality Qphred20 were kept for the enrichment analysis.

treatment_protocol: Doxycyline was administrated to samples indicated above as a concentration of 1μg/ml

tag: genotype/variation

value: Eed-/-

tag: dox treatment

value: yes

tag: cell passage

tag: antibody


title: 36:11 WT Input

description: 36:11 WT Input

value: wild type


title: 36:11 Eed-/- Input

description: 36:11 Eed-/- Input


title: 36:11 WT DOX

description: 36:11 WT DOX, JARID2


title: H2AZ-ANP32EKO

status: Public on Jan 22 2014

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

data_processing:
Base calling were performed using RTA 1.17.20 and CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 0.12.8 with the followings arguments = -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 1.4.2 with the following settings  : effective genome size = 1870000000 ; band width = 300 ; Pvalue cutoff = 10e-7 ; ChIP-seq control file : Input fraction.
Peaks detected were annotated using HOMER.
Heatmaps, global clustering and quantitative comparisons of the ChIP-seq data were performed using seqMINER. As reference coordinates, we used the MACS-determined peaks or the annotated-TSS of mouse genes. Tag densities were collected in 100 bp sliding windows spanning +/- 3 kb of the peak center or the TSS. The collected values were subjected to k-means clustering coupled to linear-based normalization.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using WigMaker version 3, tab-delimited text files contain custom tracks for UCSC genome browser.

source_name: Embryonic fibroblasts

growth_protocol: Heterozygous Anp32e+/- mice were crossed to generate wild type and Anp32e-/- MEF cells. Anp32e+/+ and Anp32e-/- MEF cells were prepared from individual embryos at embryonic day 10.5 (E10.5) bearing Anp32e+/+, Anp32e+/- and Anp32e-/- genotypes. The head and internal organs were removed, and the torso was minced and incubated in trypsin 10 min at 37°C for cell extraction. Cells were then gently pelleted, resuspended in DMEM containing 10% FBS, and plated for growth. Mouse embryonic fibroblasts (MEFs) were kept in culture for no more than 1 month before chromatin immunoprecipitation (ChIP) analysis was carried out.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. The libraries were sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions.

tag: cell type

value: Embryonic fibroblasts

tag: passages

value: 5-10 passages

tag: genotype

value: ANP32E KO

tag: chip antibody

tag: genetic background


title: TX1072 D4 dox Input

description: TX1072 D4 dox Input


title: 36:11 WT

description: 36:11 WT, JARID2

value: no


title: TX1072 D4 dox 2

description: TX1072 D4 dox 2, JARID2


title: TX1072 ES Input

description: TX1072 ES Input


title: Input-ANP32EKO

value: Input


title: Input-ANP32EWT

value: ANP32E WT


title: TX1072 ES 1

description: TX1072 ES 1, JARID2


title: TX1072 ES 2

description: TX1072 ES 2, JARID2


title: TX1072 D4 dox 1

description: TX1072 D4 dox 1, JARID2


title: H2AZ-ANP32EWT


title: KO

city: Tianjin

first: Xuexia

last: Zhou

address: 154 Anshan Road

department: Tianjin Neurological Institute

institute: Tianjin Medical University General Hospital

description: Sample 2

data_processing:
Images generated by sequencers are converted by base calling into nucleotide sequences.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were then aligned to the reference chicken genome (release: galGal4) and the corresponding recently annotated genes (galGal4.0) using the TopHat program (v2.0.6). In the alignment, preliminary experiments were performed to optimize the alignment parameters to provide the most information on the alternative splicing events.
Cufflinks was used to construct SRSF10-/- and wildtype DT40 transcriptoms and Cuffmerge merges the transcriptomes with the reference gene annotations (galGal4.0) to generate a new comphensive transcriptome.
A jave program called ASD (alternative splicing detector) was developed to detect and assess alternative splicing events between the two samples.
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text file includes the loci on chrosome, read counts, and stantistially tests for alternative splicing events between the two samples

organism: Gallus gallus

source_name: SRSF10 KO_DT40

extract_protocol:
Cells were harvested and total RNA was extracted by Trizol reagent. Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected.
Libraries for paired-end sequencing were prepared using mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

value: SRSF10-deficient (KO); SRSF10-/-

value: bursa

tag: cell line

value: lymphoblast


title: si-AR-2

tag: sample type


title: K562 TotalRNA WTAP KD Rep2

city: Los Angeles

first: Philip

middle: James

last: Uren

state: CA

address: 1050 Childs Way, RRI201

institute: University of Southern California

data_processing:
Illumina Casava 1.8.2 was used to generate fastq files
Reads were aligned to the hg18 genome using RMAP
Reads were counted to a transcriptome reference compiled from the UCSC genome browsers RefSeq track and Gene Symbols table using in-house software
Read counts were pooled for control and WTAP KD samples
Differential expression of genes and exons was calculated using a hypergeometric test; in-house software
Genome_build: hg18
Supplementary_files_format_and_content: Read counts in BED format, exon and gene diffex in BED+ format with four extra columns: pooled read count in control, pooled read count in KD, p-value and odds-ratio from statistical test
Supplementary_files_format_and_content: *readCounts.bed: Tab separated with columns: chrom, start, end, gene name, score, strand; score is the read count for the gene.
Supplementary_files_format_and_content: GeneDiffex.bed: Extended BED. Tab separated with columns: chrom, start, end, gene name, score, strand, pooled wild-type read-count, pooled WTAP KD read-count, p-value, odds-ratio
Supplementary_files_format_and_content: ExonDiffex.bed: Extended BED. Tab separated with columns: chrom, start, end, exon name, score, strand, pooled wild-type read-count, pooled WTAP KD read-count, p-value, odds-ratio

source_name: K562 cells

growth_protocol: Cells were grown in IMDM containing 10% FBS and 1% penicillin/streptomycin at 37C and 5%CO2

extract_protocol:
RNA was extracted by Trizol method followed by an extra purification step via Qiagen RNeasy Minielute columns.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatement.  K562  control and WTAP knockdown cells were utilized.

value: WTAP knocked down


title: K562 TotalRNA Rep2

value: control


title: K562 TotalRNA WTAP KD Rep1


title: K562 TotalRNA Rep1


title: WT

description: Sample 1


title: Erz

city: Fuzhou

first: Yue

last: Zhicao

state: Fujian

address: Institute of Life Sciences, Fuzhou University

department: Institute of Life Sciences

institute: Fuzhou University

data_processing:
Image analysis and basecalling was performed using the Illumina Pipeline v1.5+.
Raw sequences are transformed into Clean Tags after following steps of data-processing using customized workflow developed by Shenzhen Huada Gene Sci-Tech Company.
1. 3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences
2. Empty reads removal (reads with only 3' adaptor sequences but no tags)
3. Low quality tags removal (Tags with unknown sequences 'N')
4. Removal of tags which are too long or too short, leaving Tags of 21nt long
5. Removal of Tags with a copy number of 1 (probably be sequencing error)
6. Generate Clean Tags
A virtual libraries is build to contain all the possible CATG+17 bases length sequences of the reference gene sequences (Mus musculus genome mm10).
All clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered.
Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).
(Morrissy, A. S., R. D. Morin, et al . 2009. "Next-generation tag sequencing for cancer gene expression profiling." Genome Res.)
Genome_build: mouse genome mm10
Supplementary_files_format_and_content: text file with gene expression level

source_name: Feather epithelium

extract_protocol:
Total RNA extracted with Trizol. 4-6 ug total RNAs used for analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: feather follicle

tag: Stage

value: Feather epithelium at growth phase


title: Pp

source_name: Mesenchymal pulp

value: Mesenchymal pulp at growth phase


title: 36:11 Eed-/-

description: 36:11 Eed-/- , JARID2

value: Eed-/-


title: m24 CMS-Seq CMS pulldown

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description: CMS pulldown

data_processing:
Reads were mapped to the mm9 mouse genome using BSMAP by allowing at most four mismatches. Only uniquely mapped reads were used for MACS peak calling with a P-value cutoff of 1 × 10−5
Genome_build: mm9
Supplementary_files_format_and_content: text; BED format file which contains the peak locations called by MACS. The 5th column in this file is the -10*log10pvalue of the corresponding peak region.

source_name: 24 month Hematopoietic Stem Cells

growth_protocol: Freshly sorted 12 month wild type (Mx1-cre-;Dnmt3afl/fl) and knockout (Mx1-cre+;Dnmt3a-/-) mouse HSCs (SP-KSL-CD150+)

extract_protocol:
Extract genomic DNA using Invitrogen PureLink Genomic DNA kits
Tru-Seq DNA sample prep kit

treatment_protocol: Adapter-ligated fragments were treated with sodium bisulfite (Qiagen) and immunoprecipitated with anti-CMS antiserum

value: Murine bone marrow derived primary HSCs

tag: cell surface marker


title: m24 CMS-Seq input control

description: input control


title: ko3a CMS-Seq input control

description: input control

source_name: Dnmt3a knockout Hematopoietic Stem Cells


title: ko3a CMS-Seq CMS pulldown

description: CMS pulldown


title: mouse testis 16dpp DNA input

city: Bethesda

first: Gennady

last: Margolin

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
basecalls for mRNA samples performed using Illumina pipeline version 1.0.9
basecalls for RNA Polymerase II (RNAPII) ChIP and input performed using CASAVA version 1.7.0 (version 1.8.1 for 10dpp RNAPII ChIP - Sample 11)
only reads passing default Illumina quality filtering (PF) were used in subsequent analyses.
mRNA-Seq reads were trimmed 2 bases at both ends and the resulting 32bp reads were aligned using Illumina ELAND from pipeline 1.0.9 to mm9 genome extended to include 56bp splice junctions based on UCSC version 4 gene annotation.
Gene expression RPKM was calculated using custom Perl scripts based on version 4 of UCSC gene annotation (file kgCanon_RPKMbyDpp_clusters.txt).
Cell type expression RPKM was estimated computationally for five composite cell types: A - mostly somatic, B - spermatogonia to leptotene, C - zygotene, D - pachytene, E - post-meiotic-I (file kgCanon_RPKMbyCT_clusters.txt).
RNAPII ChIP and input reads were aligned using ELAND v2 from corresponding CASAVA distribution to mm9 genome.
RNAPII peak calling was done using MACS 2.0.9 with default parameters and merged DNA input from 6dpp and 16dpp.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using a custom script.
Supplementary_files_format_and_content: peaks.bed files were produced by MACS 2.0.9.

source_name: whole testis 16dpp

extract_protocol: Whole-testis extracts were collected from 10 and 16 dpp pups and immediately cross-linked with 1% paraformaldehyde. Cells were washed and then pelleted and sonicated in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8 and 1x Protease Inhibitor Cocktail (Roche) for 16 cycles at 15 sec on and 15 sec off in a sonicator water bath (Bioruptor Diagenode) at 4°C. After dialysis samples were incubated with antibody-coated magnetic beads (Dynabeads M-280 Invitrogen) overnight at 4°C. Immunoprecipitated chromatin on magnetic beads was washed and then eluted in elution buffer (1% SDS, 100 mM NaHCO3) for 15 min at 65°C and reverse cross-linked overnight at 65°C with 200 mM NaCl. Proteinase K treated reverse cross-linked DNA was purified with MinElute PCR purification kit (Qiagen) folllowed by standard DNA library construction protocol (Illumina).

tag: tissue

value: testis

value: post natal day 16

tag: Sex

value: male

value: wild type

value: none, input


title: STAT1 WT Th0 IFNb

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

description: STAT1 from IFNb treated

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 genomes using the Illumina Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp (SICER).
Peaks: Peak detection was performed with SICER (Zang et al., 2009 Bioinformatics, 25:1952-1958) and MACS.
Genome_build: mm9
Supplementary_files_format_and_content: STAT1_WT_Th0_IFNb_peaks.bedgraph: Peak file called by MACS.
Supplementary_files_format_and_content: STAT1_WT_IFN_SICER.bedgraph: Peak file called by SICER.

source_name: primary CD4+ T cells from spleen and lymph nodes

growth_protocol: Naïve CD4+CD25-CD44-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured with plate-bound anti-CD3 and anti-CD28 (10 ug/ml each), anti-IFNg (10ug/ml), anti-IL-4 (10 ug/ml) and IFNb (5000 U/ml) for 3 days.

extract_protocol:
Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase 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 HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: After 3 day culture in vitro, cells were restimulated for 2hr with IFNb (5000 U/ml) before harvest of the cells.

tag: strain

value: C57BL/6J (wild type)

value: CD4+ T cell

value: spleen and lymph node pooled

value: FACS sorted naive CD4+T cells

value: STAT1(sc-592, SantaCruz)


title: mouse testis 10dpp RNAPII ChIP

source_name: whole testis 10dpp

tag: age

value: post natal day 10

value: rabbit polyclonal anti-RNA polymerase II (N-20) (santa cruz sc-899)


title: DP_Resting

source_name: Dermal Papilla

value: feather follicle

value: Dermal Papilla at resting phase


title: DP_Growth

value: Dermal Papilla at growth phase


title: Runx3_IL-15NK_CHIP_NIS

city: Rehovot

first: Joseph

last: Lotem

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

description: IP experiment of NIS

data_processing:
CASAVA 1.8.2
For data analysis ~60 and 54 million Runx3 and NIS IP short read (50 bp) sequences, respectively, were aligned uniquely to the mouse genome (mm9) using ELAND. Peaks of enriched Runx3 regions were detected using the uniquely aligned sequences (sorted file) of IP versus the NIS, using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file containing Runx3 peaks detected by MACS1.4 done by scaling to small.

source_name: Splenic NK cells

growth_protocol: ChIP-Seq experiments for detection of Runx3-bound genomic regions were conducted using in-house anti Runx3 Ab on 40 million isolated splenic NK cells from mice injected twice with IL-15/Ra complexes, 2 days apart. NK cells were isolated by negative  selection using NK cell isolation kit (R&D) and sorting for NKp46+ cells. Isolated NK cells were fixed and frozen at  -80°C.

extract_protocol:
Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~200bp. For immunoprecipitation, 48ul of anti-Runx3 Ab or NIS were added to 12 mL of diluted, fragmented chromatin. DNA was purified using QIAquick spin columns (QIAGEN).
For ChIP-seq analysis, ChIP-seq libraries were prepared using the ChIP-Seq sample preparation kit (IP-102-1001, illumina) according to the manufactures instructions. Illumina sequencing was performed using Illumina HiSeq2000 platform according to the manufactures instructions by loading 9 pmoles of denatured library template onto separate lanes of a flow cell. Sequencing short reads (50 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).

value: Splenic NK cells

value: Cells were freshly isolated, fixed and frozen at -80°C.

value: ICR

value: Non-immune rabbit serum


title: Day4_regeneration

source_name: feather follicle

value: feather follicle  at regeneration phase by 4 days after wound


title: mouse testis 16dpp RNAPII ChIP

value: testis

value: post natal day 16

value: male

value: wild type

value: rabbit polyclonal anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (Abcam ab5131)


title: Day2_regeneration

value: feather follicle at regeneration phase by 2 days after wound


title: mouse testis 6dpp DNA input

source_name: whole testis 6dpp

value: post natal day 6

value: none, input


title: mouse testis 20dpp mRNA

source_name: whole testis 20dpp

extract_protocol: Total RNA was purified using Total RNA Isolation Mini Kit (Agilent). 20 μg of total RNA was loaded on 100 ul oligo(dT) Dynabeads (Dynal) and polyA+ fraction was eluted in 15 μl of DEPC-treated water. 0.5 μg aliquots of polyA+ RNA were fragmented in total volume of 10 μl of RNA fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOA) for 2 min at 95°C. First and second strand cDNA synthesis was performed using SuperScript double-stranded cDNA synthesis kit (Invitrogen) using 150 ng of fragmented RNA and 500 ng of random hexamers (Promega). Standard Illumina protocol was used to construct sequencing library.

value: mixed C57BL/6 and 129

value: post natal day 20


title: Runx3_IL-15NK_CHIP_Runx3_IP

description: IP experiment of Runx3

value: Runx3 poly clonal home made


title: mouse testis 38dpp mRNA

source_name: whole testis 38dpp

value: post natal day 38


title: mouse testis 18dpp mRNA

source_name: whole testis 18dpp

value: post natal day 18


title: mouse testis 12dpp mRNA

source_name: whole testis 12dpp

value: post natal day 12


title: mouse testis 16dpp mRNA


title: mouse testis 10dpp mRNA

value: post natal day 10


title: HeLa - 8 Hr Replicate #1

status: Public on Jan 21 2014

city: Pullman

first: Douglas

middle: Ruben

last: Call

state: Washington

address: 240 SE Ott Rd

department: Paul G. Allen School for Global Animal Health

institute: Washington State University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with removal of failed reads and was then mapped to reference genomes for V. parahaemolyticus strain RIMD 2210633 chromosomes 1 and 2 (NCBI Reference Sequence NC_004603.1 and NC_004605.1, respectively) using CLC Genomics Workbench (version 6.0.5)
Mapping for RNA-Seq was allowed 20 additional upstream and downstream bases for each gene and a paired distance range of 0-300 bases, with up to 2 mismatches, 90% alignment and 80% similarity required for inclusion as a mapped read
Genome_build: V. parahaemolyticus strain RIMD 2210633 chromosomes 1 and 2 (NCBI Reference Sequence NC_004603.1 and NC_004605.1)
Supplementary_files_format_and_content: Text files include RPKM values for each sample

organism: Vibrio parahaemolyticus

source_name: Bacterial culture, HeLa - 8 Hr

extract_protocol:
Total RNA was extracted using a RiboPure-Bacteria kit (Ambion, Cat #AM1925) with the addition of a second treatment of DNase using a TURBO DNA-free kit (Ambion, Cat #AM1907) and then mRNA purified using a Ribo-Zero Magnetic kit (Gram-Negative Bacteria) (Epicentre, Cat #MRZGN126)
mRNA libraries were prepared for sequencing using a TruSeq RNA Sample Prep kit (Illumina, Cat #RS-122-2001)

treatment_protocol: 0 hr culture used to infect 80-100% confluent HeLa cells for 8 hr at MOI ~10-20.  Triplicate infection wells were removed with cell scraper and pooled.

tag: serotype

tag: genotype/variation

value: Wild-type


title: mouse testis 6dpp mRNA


title: Treated replicate 2

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
The quality of raw sequence data was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).   No additional processing of the primary data was required.
Paired end sequences were aligned to the Tbb genome (obtained from ftp.sanger.ac.uk/pub4/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_WGS_24_08_2012/chromosomes/ ) using bowtie2 (parameters: --very-sensitive-local; version: 2.0.2), piped through samtools (parameters: -bhS; version: 0.1.18), and stored in indexed BAM format.
The annotated Tbb genome was viewed using Artemis software (http://www.sanger.ac.uk/resources/software/artemis/ ; http://ukpmc.ac.uk/abstract/MED/11120685), and coding segment (CDS) region coordinates extracted prior to conversion to bedtools bedfile format.  Bedtools (paramters: multicov -bams ; version: bedtools 2.15.0) was used to generate coverages for each CDS for each sample replicate.  RPKM-like values were calculated by dividing coverage by CDS size.
Statistical analyses of the two sample groups were undertaken in the R environment (www.R-project.org) using Bioconductor (www.bioconductor.org) packages.  Differential expression was explored using linear models and empirical Bayes methods, using the limma package (Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3. (Online, Tech Report PDF)).  RPKM-like values were offset by 1, logged, and quantile normalised prior to group-wise comparison.  Post-comparison,  data were filtered to remove loci whose normalised mean RPKM-like values were below the 10% quantile for all samples (8723 retained, 955 discarded).
Genome_build: ftp.sanger.ac.uk/pub4/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_WGS_24_08_2012/chromosomes/
Supplementary_files_format_and_content: Annotated, normalised mean RPKM values

organism: Trypanosoma brucei brucei

source_name: CAT-PAD1 3’UTR GUS-Const 3’UTR cells

growth_protocol: Trypanosomes were grown in HMI-9 with 20% FCS at 37°C in 5% CO2

extract_protocol:
RNA samples for RNA sequencing were harvested from CAT-PAD1 3’UTR GUS-Const 3’UTR cells.
Library construction and sequencing was carried out by BGI-Hong Kong using the Illumina® TruSeq™ RNA Sample Preparation Kit.

treatment_protocol: Cells were treated with either 50µM DDD00015314 or 0.5% v/v DMSO for 24 hours.

value: monomorphic slender

value: Lister S427

tag: treatment


title: Treated replicate 1


title: Control replicate 2

value: 0.5% v/v DMSO


title: Control replicate 1


title: mouse testis 14dpp mRNA

source_name: whole testis 14dpp

value: testis

value: post natal day 14

value: male


title: HeLa - 8 Hr Replicate #2


title: HeLa - 3 Hr Replicate #1

source_name: Bacterial culture, HeLa - 3 Hr

treatment_protocol: 0 hr culture used to infect 80-100% confluent HeLa cells for 3 hr at MOI ~10-20.  Triplicate infection wells were removed with cell scraper and pooled.


title: HeLa - 3 Hr Replicate #2


title: HeLa - 4 Hr Replicate #2

source_name: Bacterial culture, HeLa - 4 Hr

treatment_protocol: 0 hr culture used to infect 80-100% confluent HeLa cells for 4 hr at MOI ~10-20.  Triplicate infection wells were removed with cell scraper and pooled.


title: HeLa - 0 Hr Replicate #2

source_name: Bacterial culture, HeLa - 0 Hr

treatment_protocol: 16 hr culture was diluted 1:50 into LB-S, incubated at 37°C with shaking for 1.5 hr, centrifuged and pellet resuspended in equivalent volume of HBSS supplemented with 1% FBS (v/v)


title: DMEM Replicate #2

source_name: Bacterial culture, DMEM

treatment_protocol: 1 mL of 16 hr culture was centrifuged and pellet resuspended 1:10 in DMEM supplemented with 1% FBS (v/v) and incubated at 37°C with shaking for 3 hr


title: HeLa - 6 Hr Replicate #1

source_name: Bacterial culture, HeLa - 6 Hr

treatment_protocol: 0 hr culture used to infect 80-100% confluent HeLa cells for 6 hr at MOI ~10-20.  Triplicate infection wells were removed with cell scraper and pooled.


title: HeLa - 6 Hr Replicate #2


title: ExsD Replicate #2

source_name: Bacterial culture, ExsD

treatment_protocol: 16 hr culture was diluted 1:1000 into LB-S containing chloramphenicol (8.5 µg/ml), incubated to OD600 of 0.3-0.5, IPTG added to 1 mM and incubated at 37°C with shaking for 3 hr

value: Wild-type containing exsD gene located on plasmid pMMB207


title: ExsA Replicate #1

source_name: Bacterial culture, ExsA

value: Wild-type containing exsA gene located on plasmid pMMB207


title: HeLa - 0 Hr Replicate #1


title: HeLa - 2 Hr Replicate #1

source_name: Bacterial culture, HeLa - 2 Hr

treatment_protocol: 0 hr culture used to infect 80-100% confluent HeLa cells for 2 hr at MOI ~10-20.  Triplicate infection wells were removed with cell scraper and pooled.


title: HeLa - 2 Hr Replicate #2


title: Zebrafish_Hoxd10a

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

institute: EPFL

description: library strategy: 4C-Seq

data_processing:
Reads were mapped to the mm9 (NCBIM37) Mouse genome assembly, to the Zf9 Zebrafish genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
De-multiplexing, mapping and 4C-analysis were performed through HTSstation (http://htsstation.epfl.ch) according to previously described procedure (Noordermeer et al., 2011).
Figures were made using a running mean algorithm using a window size of eleven fragments. 4C tracks were normalized to the same total intensity over the regions visualuzed in the figures, such as to see only changes in contacts distribution and to minimize PCR complexity bias in each samples. .
Both the mapping and the 4C-seq analysis were done through HTSstation (http://htsstation.epfl.ch/).
Genome_build: mouse: MGSCv37
Genome_build: zebrafish: Zv9
Supplementary_files_format_and_content: density files (bedGraph) and smoothed/normalized data (bedGraph), one per viewpoint, per tissue

organism: Danio rerio

source_name: Whole embryo 5dpf

extract_protocol:
4C–seq libraries were constructed as described before (Noordermeer et al. 2011). Mouse libraries consisted of 52 dissected E12.5 proximal forelimb buds, distal forelimb buds or forebrains. Zebrafish libraries consisted of approximately 300 5 dpf embryos from the TU strain. For mouse viewpoints, the primary restriction enzyme used was NlaIII (New England Biolabs, R0125L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543M). For zebrafish viewpoints, the primary restriction enzyme was DpnII (New England Biolabs, R0543M) and the secondary enzyme was TaqαI (New England Biolabs, R0149M) (using the latter enzyme DNA was cut for 8 hours at 65°C). For each viewpoint between 1.3 and 2.6 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences. Multiplexed samples were sequenced on the Illumina HiSeq system using 100 bp single-end reads according to the manufacturer’s specifications. 4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline of the BBCF HTSstation (available at http://htsstation.epfl.ch and discussed in (Noordermeer et al. 2011)). Mouse samples were mapped to the ENSEMBL Mouse assembly NCBIM37 (mm9) and zebrafish samples were mapped to the ENSEMBL Zebrafish assembly Zv9.
4C PCR was sequenced with Illumina Genome AnalyzerHiSeq 2000. Data was mapped to the mouse genome using HTSstation (http://htsstation.vital-it.ch/).

value: TU

value: Whole embryo

value: 5 dpf

value: wild type


title: Zebrafish_Hoxd13a

description: library strategy: 4C-Seq


title: ExsD Replicate #1


title: ExsA Replicate #2


title: DMEM Replicate #1


title: Zebrafish_Hoxa11b

description: library strategy: 4C-Seq


title: LB-S Replicate #1

source_name: Bacterial culture, LB-S

treatment_protocol: 16 hr culture was diluted 1:100 into LB-S and incubated at 37°C with shaking for 3 hr


title: Zebrafish_Hoxa11a

description: library strategy: 4C-Seq


title: LB-S Replicate #2


title: Mouse_Brain_Hoxd13

description: library strategy: 4C-Seq

source_name: Brain E12.5

value: Brain


title: Mouse_Brain_Hoxd4

description: library strategy: 4C-Seq


title: RPL11-MO

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

description: Sample 2

data_processing:
TopHat for mapping of Hiseq 2000 RNA-Seq data
Cufflinks for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples
Computation and visualization were achieved using the heatmap plus package in R.
IPA and the Gene Ontology for functional analysis of specific genes
Genome_build: Zv9
Supplementary_files_format_and_content: The .txt files report FPKM.

source_name: embryo, RPL11-deficient

growth_protocol: Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf

extract_protocol:
Immediately after harvesting, 40-50 pooled embryos at 48 hpf from different experiment replicates were snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from the pooled embryos using TRIzol (Invitrogen) according to the manufacturer’s instructions.
mRNA libraries were constructed using the Illumina mRNA-Seq library preparation kit according to the manufacturer’s instructions.

treatment_protocol: Zebrafish embryos at the one-cell stage were injected with the MOs using an Microinjector (WPI SYS-PV830). Based on initial injection trials, 2-5 ng MO and control MO was chosen as the optimal concentration.

tag: developmental stage

value: embryo

value: RPL11 morpholino knockdown


title: morpholino-control

description: Sample 1

source_name: embryo, control

value: control morpholino


title: Mouse_Brain_Hoxd11

description: library strategy: 4C-Seq


title: Zebrafish_Hoxd11a

description: library strategy: 4C-Seq


title: Mouse_Brain_Hoxa11

description: library strategy: 4C-Seq


title: Mouse_Brain_Hoxa4

description: library strategy: 4C-Seq


title: Mouse_Brain_Hoxa13

description: library strategy: 4C-Seq


title: Zebrafish_Hoxd4a

description: library strategy: 4C-Seq


title: Zebrafish_Hoxa2b

description: library strategy: 4C-Seq


title: Zebrafish_Hoxa4a

description: library strategy: 4C-Seq


title: HeLa - 4 Hr Replicate #1

value: Wild-type


title: Mouse_Autopod_Hoxd11

description: library strategy: 4C-Seq

source_name: Autopod E12.5

value: Autopod


title: Zebrafish_Hoxa9a

description: library strategy: 4C-Seq


title: Zebrafish_Hoxa13b

description: library strategy: 4C-Seq


title: Mouse_Autopod_Hoxa4

description: library strategy: 4C-Seq


title: Mouse_Autopod_Hoxd13

description: library strategy: 4C-Seq


title: Zebrafish_Hoxa13a

description: library strategy: 4C-Seq


title: Mouse_Proximal_limb_Hoxd4

description: library strategy: 4C-Seq

source_name: Proximal limb E12.5

value: Proximal limb


title: Mouse_Proximal_limb_Hoxd11

description: library strategy: 4C-Seq


title: Mouse_Autopod_Hoxa13

description: library strategy: 4C-Seq


title: Mouse_Autopod_Hoxd4

description: library strategy: 4C-Seq


title: Mouse_Autopod_Hoxa11

description: library strategy: 4C-Seq


title: Mouse_Brain_Hoxa9

description: library strategy: 4C-Seq


title: Mouse_Autopod_Hoxa9

description: library strategy: 4C-Seq


title: Mouse_Proximal_limb_Hoxd13

description: library strategy: 4C-Seq


title: Mouse_Proximal_limb_Hoxa4

description: library strategy: 4C-Seq


title: Mouse_Proximal_limb_Hoxa13

description: library strategy: 4C-Seq


title: MeDIP-seq data_34816

city: London

first: Matthew

middle: N

last: Davies

state: Greater London

address: St Thomas' Hospital Campus

department: Twin Research

institute: King's College London

data_processing:
Basecalls performed using CASAVA version 1.4
MeDIP-seq reads were aligned to the hg19 genome assembly using bwa
Genome_build: hg19
bed files were generated from bam files using the bedtools package
Supplementary_files_format_and_content: RPKM files were generated from bed files using the MEDIPS R package

source_name: monozygotic twin pair_MDD case

extract_protocol:
Whole blood samples were collected from the twins and stored at -80°C in EDTA tubes. DNA was extracted from 2 x 6ml EDTA blood using the Nucleon Genomic DNA Extraction Kit BACC3 and stored at -20°C in TE Buffer.
BGI protocol

tag: twin pair

tag: subject status

value: major depressive disorder

value: whole blood sample


title: Mouse_Proximal_limb_Hoxa11

description: library strategy: 4C-Seq

tag: genotype


title: MeDIP-seq data_34815

source_name: monozygotic twin pair_Control

value: Control


title: MeDIP-seq data_33876


title: Mouse_Proximal_limb_Hoxa9

description: library strategy: 4C-Seq


title: MeDIP-seq data_33019


title: MeDIP-seq data_33430


title: MeDIP-seq data_33429


title: MeDIP-seq data_33018


title: MeDIP-seq data_32461


title: MeDIP-seq data_31351


title: MeDIP-seq data_32460


title: MeDIP-seq data_31350


title: MeDIP-seq data_31288


title: MeDIP-seq data_30551


title: MeDIP-seq data_30144


title: MeDIP-seq data_29423


title: MeDIP-seq data_29424


title: MeDIP-seq data_30143


title: MeDIP-seq data_28530


title: MeDIP-seq data_28310


title: MeDIP-seq data_28531


title: MeDIP-seq data_30085


title: MeDIP-seq data_28260


title: MeDIP-seq data_27768


title: MeDIP-seq data_33877


title: MeDIP-seq data_27767


title: MeDIP-seq data_28309


title: MeDIP-seq data_28259


title: MeDIP-seq data_26419


title: MeDIP-seq data_27762


title: MeDIP-seq data_26738


title: MeDIP-seq data_31428


title: MeDIP-seq data_26737


title: MeDIP-seq data_27761


title: MeDIP-seq data_26420


title: MeDIP-seq data_26418


title: MeDIP-seq data_26417


title: MeDIP-seq data_26005


title: MeDIP-seq data_26006


title: MeDIP-seq data_25770


title: MeDIP-seq data_25771


title: MeDIP-seq data_30550


title: MeDIP-seq data_30086


title: MeDIP-seq data_24984


title: MeDIP-seq data_24983


title: MeDIP-seq data_24676


title: MeDIP-seq data_22255


title: MeDIP-seq data_24675


title: MeDIP-seq data_24652


title: MeDIP-seq data_24653


title: MeDIP-seq data_22254


title: MeDIP-seq data_18838


title: MeDIP-seq data_21681


title: MeDIP-seq data_21680


title: Pro-AR_wt1

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

description: Chromatin IP against AR

data_processing:
Alignment: Sequence reads were obtained, purity filtered using the Illumina Genome Analyzer Pipeline and mapped to the mouse (mm9) genomes using BOWTIE with parameters -n0, -k1, -l30.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS2, https://github.com/taoliu/MACS/) and HOMER (http://biowhat.ucsd.edu/homer/) algorithms. Overlapping peaks called from MACS (FDR<5%) and HOMER (FDR<2%) were used in downstream analysis. Processed peak files are included for overlapping MACS2 and HOMER peaks.
Genome_build: mm9
Supplementary_files_format_and_content: Processed peak files in BED format

growth_protocol: Mice were housed in standard 12-h light-dark cycle and were fed ad libitum.

extract_protocol: Lysates were clarified from sonicated nuclei and DNA-protein complexes were isolated with respective antibodies. Libraries were prepared according to Illumina's instructions. 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 20 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: Tissues were harvested from intact adult male mice.

value: ventral prostate

value: 12 weeks old

value: Intact

tag: chip antibody

value: AR (Sahu et al. 2011)


title: Pro-rIgG

description: Chromatin IP against non-specific IgG

source_name: Pro-rIgG

value: rIgG (sc-2027, SantaCruz)


title: Pro-AR_SPARKI1

description: Chromatin IP against AR

value: SPARKI


title: H3K4me1_Kid

description: Chromatin IP against H3K4me1 histone modification

data_processing:
Alignment: Sequence reads were obtained, purity filtered using the Illumina Genome Analyzer Pipeline and mapped to the mouse (mm9) genomes using BOWTIE with parameters -n0, -k1, -l30.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).   The wiggle files from MACS are submitted as processed data files for H3K4me1 and H3K27ac ChIP-seq.
Genome_build: mm9
Supplementary_files_format_and_content: Processed wiggle files from MACS

treatment_protocol: Tissues were harvested from intact adult male mice or from castrated male mice after 2-h testosterone- or vehicle-treatment.

value: wild type ICR

value: kidney

value: 8-12 weeks old

value: castrated+testosterone

value: H3K4me1 (ab8895, Abcam)


title: H3K27ac_Epi

description: Chromatin IP against H3K27ac histone modification

value: caput epididymis

value: intact

value: H3K27ac (ab4729, Abcam)


title: H3K4me1_Epi


title: rIgG1

description:
Chromatin IP against non-specific IgG
sample 5

data_processing:
Alignment: Sequence reads were obtained, purity filtered using the Illumina Genome Analyzer Pipeline and mapped to the mouse (mm9) genomes using BOWTIE with parameters -n0, -k1, -l30.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS2, https://github.com/taoliu/MACS/) and HOMER (http://biowhat.ucsd.edu/homer/) algorithms. The biological replicate lanes for each sample and IgG were concataned before peak calling and overlapping peaks called from MACS (FDR<5%) and HOMER (FDR<2%) were used in downstream analysis. Processed peak files are included for MACS2 peaks, HOMER peaks and overlapping peaks.
Genome_build: mm9
Supplementary_files_format_and_content: Processed peak files in BED format

source_name: rIgG

value: wild type


title: rIgG2

description:
Chromatin IP against non-specific IgG
sample 6


title: H3K27ac_Kid


title: H3K27ac_Pro

value: prostate


title: H3K4me1_Pro


title: mIgG1 [caput epididymis, intact]

description: Chromatin IP against mouse IgG

data_processing:
Alignment: Sequence reads were obtained, purity filtered using the Illumina Genome Analyzer Pipeline and mapped to the mouse (mm9) genomes using BOWTIE with parameters -n0, -k1, -l30.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). The technical replicate lanes assigned as a and b for each sample and IgG were concataned wherever required before peak calling. Overlapping peaks present in both biological replicates with a 2% FDR cutoff were used in downstream analysis. The peak files from MACS are submitted as tab-delimited text files.
Genome_build: mm9
Supplementary_files_format_and_content: Processed peak files in tab-delimited text format

value: mIgG (sc-2025, SantaCruz)


title: AR_wt1

description:
Chromatin IP against AR
sample 1
processed file (peaks): WT_AR_vs_IgG_macs2_peaks_FDR5.bed
processed file (peaks): WT_AR_vs_IgG_homer_peaks_FDR2.bed
processed file (peaks): WT_AR_vs_IgG_macs2_homer_ovl_peaks.bed


title: AR_wt2

description:
Chromatin IP against AR
sample 2
processed file (peaks): WT_AR_vs_IgG_macs2_peaks_FDR5.bed
processed file (peaks): WT_AR_vs_IgG_homer_peaks_FDR2.bed
processed file (peaks): WT_AR_vs_IgG_macs2_homer_ovl_peaks.bed


title: AR_SPARKI1

description:
Chromatin IP against AR
sample 3
processed file (peaks): SPARKI_AR_vs_IgG_macs2_peaks_FDR5.bed
processed file (peaks): SPARKI_AR_vs_IgG_homer_peaks_FDR2.bed
processed file (peaks): SPARKI_AR_vs_IgG_macs2_homer_ovl_peaks.bed


title: rIgG1 [caput epididymis, intact]

description: Chromatin IP against rabbit IgG


title: Hnf4a_Intact [caput epididymis, intact]

description: Chromatin IP against HNF4a

value: HNF4a (ab41898, Abcam)


title: FoxA1_Intact [caput epididymis, intact]

description: Chromatin IP against FOXA1

value: FOXA1 (ab23738, Abcam)


title: AP2a_Cast1b [caput epididymis, castrated+vehicle]

description: Chromatin IP against AP2a

value: castrated+vehicle

value: AP2a (ab52222, Abcam)


title: AP2a_Intact_rep2 [caput epididymis, intact]

description: Chromatin IP against AP2a


title: AR_Intact_rep1 [caput epididymis, intact]

description: Chromatin IP against AR

value: AR (Sahu et al. 2011)


title: AP2a_Cast1a [caput epididymis, castrated+vehicle]

description: Chromatin IP against AP2a


title: AR_Intact_rep2 [caput epididymis, intact]

description: Chromatin IP against AR


title: AP2a_Intact_rep1 [caput epididymis, intact]

description: Chromatin IP against AP2a


title: rIgG1 [kidney, castrated+testosterone]

description: Chromatin IP against rabbit IgG

value: rIgG (sc-2027, SantaCruz)


title: AR_Cast1 [caput epididymis, castrated+vehicle]

description: Chromatin IP against AR

value: wild type ICR


title: Hnf4a_Cast+T [kidney, castrated+testosterone]

description: Chromatin IP against HNF4a

value: kidney


title: Hnf4a_Cast1b [kidney, castrated+vehicle]

description:
Chromatin IP against HNF4a
Hnf4a_Kid_Cast1_peaks.txt

value: 8-12 weeks old


title: AR_SPARKI2

description:
Chromatin IP against AR
sample 4
processed file (peaks): SPARKI_AR_vs_IgG_macs2_peaks_FDR5.bed
processed file (peaks): SPARKI_AR_vs_IgG_homer_peaks_FDR2.bed
processed file (peaks): SPARKI_AR_vs_IgG_macs2_homer_ovl_peaks.bed

value: SPARKI

value: 12 weeks old

value: Intact


title: Hnf4a_Cast1a [kidney, castrated+vehicle]


title: AR_Cast+T_rep1 [kidney, castrated+testosterone]

description: Chromatin IP against AR

value: castrated+testosterone


title: mIgG1 [prostate, castrated+testosterone]

description: Chromatin IP against mouse IgG


title: AR_Cast1 [kidney, castrated+vehicle]

description: Chromatin IP against AR


title: MeDIP-seq data_18837

value: major depressive disorder

value: whole blood sample


title: rIgG1a [prostate, castrated+vehicle]

description: Chromatin IP against rabbit IgG

value: prostate


title: AP2a_Cast+T [prostate, castrated+testosterone]

description: Chromatin IP against AP2a


title: FoxA1_Cast+T_rep2 [prostate, castrated+testosterone]

description: Chromatin IP against FOXA1


title: FoxA1_Cast [prostate, castrated+vehicle]

description: Chromatin IP against FOXA1


title: Hnf4a_Cast+T [prostate, castrated+testosterone]

description: Chromatin IP against HNF4a


title: FoxA1_Cast+T_rep1 [prostate, castrated+testosterone]

description: Chromatin IP against FOXA1


title: siGATA2-AR_ChIP Seq

city: Columbus

first: Qianben

last: Wang

state: Ohio

address: 460 W 12th Avenue

department: Molecular and Cellular Biochemistry and the Comprehensive Cancer Center

institute: Ohio State University

description: Sample 2

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.0 with parameters '-k 2 -v 2' to report up to two valid alignments
Read with multiple valid alignments were removed using a Perl program
Uniquely mapped reads from replicates of the same sample were pooled
Peaks were called using MACS v1.4.2 with parameters '-m 3,30 -g hs -p 1e-8'
Genome_build: hg19
Supplementary_files_format_and_content: wig

source_name: prostate cell line

growth_protocol: LNCaP cells were cultured in 10% FBS RPMI 1640 medium, 1:2.5 split every 2 days. Cells are cultured in 5% charcoal stripped FBS rpmi 1640 medium

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-DNA or FoxA1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#15023092 ). Briefly, DNA was end-repaired, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, the DNA was size selected from an agarose gel and was PCR amplified with Illumina primers for 15 cycles. Libraries were sequenced on the Hi-seq 2500 following the manufacturer's protocols.

treatment_protocol: LnCaP cells were treated with 40nM siControl or siGATA2 from Dharmacon company for 3 days. For AR ChIP, 1 nM R1881 was added before cell colllection for ChIP assay.

value: androgen-dependent prostate cancer derived cell line LNCaP

tag: passage number

value: AR [Santa cruz sc-816 (N-20) lot# D0513]


title: AR_Cast+T_rep2a [prostate, castrated+testosterone]

description:
Chromatin IP against AR
AR_Pro_Cast+T_rep2_peaks.txt


title: mIgG1 [kidney, castrated+testosterone]

description: Chromatin IP against mouse IgG

value: mIgG (sc-2025, SantaCruz)


title: AP2a_Cast+T [kidney, castrated+testosterone]

description: Chromatin IP against AP2a


title: AR_Cast+T_rep2b [prostate, castrated+testosterone]


title: AR_Cast+T_rep2 [kidney, castrated+testosterone]

description: Chromatin IP against AR


title: AR_Cast1a [prostate, castrated+vehicle]

description:
Chromatin IP against AR
AR_Pro_Cast1_peaks.txt

value: castrated+vehicle


title: AR_Cast1b [prostate, castrated+vehicle]


title: FoxA1_Cast+T [kidney, castrated+testosterone]

description: Chromatin IP against FOXA1

value: FOXA1 (ab23738, Abcam)


title: AR_Cast+T_rep1a [prostate, castrated+testosterone]

description:
Chromatin IP against AR
AR_Pro_Cast+T_rep1_peaks.txt

value: AR (Sahu et al. 2011)


title: siControl-AR_ChIP Seq

description: Sample 1

tag: cell line

value: AR [Santa cruz sc-816 (N-20) lot# D0511]

value: siControl


title: Mouse_ESCs_MLL2-/-_4d_atRA_RNA-Seq

status: Public on Jan 20 2014

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

description:
fragmentented two times Poly(A) selected ds_cDNA
Sample 27

data_processing:
Initial data processing, base calling, and alignment to the mouse reference genome was performed using the Illumina Analysis Pipeline allowing one mismatch. Only tags aligning to one position on the genome were considered for further analysis.
For RNA-seq, further analysis was performed with the 35 bp aligned sequence.
For this ChIP-Seq, the uniquely mapped sequence reads were directionally extended to 200 bp, the estimated median length of the original DNA library. If multiple tags mapped on the same genomic position, only one was included for further analysis.
The ChIP-Seq data was converted to Browser Extensible Data (BED) files for downstream analysis. To compensate for differences in sequencing depth and mapping efficiency among samples, the total number of unique reads of each sample was uniformly equalized relative to the sample with the lowest number of sequence reads, allowing quantitative comparisons.
Wiggle (WIG) files for viewing the data in the UCSC Genome Browser were generated from the normalized files.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated according to general instructions and were used for analysis; Wig files can be directly uploaded to the UCSC genome browser.

molecule: polyA RNA

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: ES cells were cultured without feeders in the presence of leukemia inhibitory factor (LIF) either in Glasgow modification of Eagles medium (GMEM) containing 10% fetal calf serum; 3 samples include the use of 2i

extract_protocol:
Experiments were performed with 3.3 million cells and 3 microgram antibody per ChIP. Crosslinking was performed on the culture plates for 20 min and ChIP’ed DNA was purified by Qiaquick PCR purification Kit (QIAGEN). Total RNA was isolated using Trizol (Invitrogen) and subjected to chloroform extraction, isopropanol precipitation and ethanol washing according to the manufacturer's recommendations. 100µg total RNA was subjected to two rounds of poly(A) selection using the Oligotex mRNA Mini Kit (Qiagen), followed by DNaseI treatment (Qiagen). 100-200ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 seconds and purified using the RNAeasy Minelute Kit (Qiagen). The fragmented mRNA was used as template for cDNA synthesis using 5µg random hexamers using Superscript III Reverse Transcriptase (Invitrogen) according to the manufacturer's recommendations. Ds-cDNA was synthesized in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified using the Minelute Reaction Cleanup Kit (Qiagen). Quality control was performed by qPCR.
DNA samples from ChIP-Seq and RNA-Seq were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Integrity of DNA libraries was confirmed by running the products on a Bioanalyzer (BioRad). Cluster generation and sequencing was performed with the Illumina Genome Analyzer IIx (GAIIx) or HiSeq 2000 sequencing platform according to standard Illumina protocols.

treatment_protocol: Recombineering, gene targeting, BAC transgenesis, chromatin immunoprecipitation and generic affinity purification to the GFP tag were performed as previously described (Fu et al., 2010; Hofemeister et al., 2011). The Mll2-/- (Lubitz et al., 2007) and Mll1-/- ESCs were derived from E14TG2a by consecutive rounds of gene targeting using the same targeting construct for the second allele after exchanging the neomycin resistance gene for hygromycin by recombineering. The Mll2F/F:CreERT2/+ and Mll1F/F:Mll2F/F:CreERT2/+ ESCs were established de novo from blastocysts after germline transmission of targeted R1 ESCs and crossing to C57Bl/6 at least five times including a cross to a C57Bl/6 Rosa26CreERT2 mouse line (Seibler et al., 2003).

tag: strain background

tag: treated with

value: atRA for 4 days

tag: cell type

value: Embryonic Stem Cells (ESCs)


title: rIgG1b [prostate, castrated+testosterone]

description: Chromatin IP against rabbit IgG

value: wild type ICR

tag: tissue

value: 8-12 weeks old

value: rIgG (sc-2027, SantaCruz)


title: Mouse_ESCs_MLL2_FC/FC_H3K27me3

description: Sample 19

value: induced Mll2 -/-

tag: chip antibody vendor

value: Upstate (Millipore)

tag: chip antibody cat. #

value: Polyclonal 07-449

tag: chip antibody lot #

value: lot 6523 Rabbit 5th bleed, exsang., 5/12/03


title: Mouse_ESCs_MLL2_F/F_H3K27me3

description: Sample 20

value: inducible Mll2 -/- (but not induced)


title: E14_4d_atTRA_RNA-Seq

description:
fragmentented two times Poly(A) selected ds_cDNA
Sample 25

value: wildtype


title: Mouse_ESCs_MLL1-/-_RNA-Seq

description:
fragmentented two times Poly(A) selected ds_cDNA
Sample 23


title: Mouse_ESCs_MLL1-/-_4d_atRA_RNA-Seq

description:
fragmentented two times Poly(A) selected ds_cDNA
Sample 26


title: E14_RNA-Seq

description:
fragmentented two times Poly(A) selected ds_cDNA
Sample 22


title: E14_7d_atRA_H3K4me3

description: Sample 15

value: atRA for 7 days

value: Diagenode


title: Mouse_ESCs_MLL2-/-_7d_atRA_H3K4me3

description: Sample 16


title: Mouse_ESCs_MLL2-/-_H3K27me3

description: Sample 18


title: E14_4d_atRA_H3K4me3

description: Sample 11


title: E14_H3K27me3

description: Sample 17


title: Mouse_ESCs_MLL1&MLL2_FC/FC_4d_atRA_H3K4me3

description: Sample 14

value: induced Mll1 -/- and Mll2 -/-


title: Mouse_ESCs_MLL2-/-_RNA-Seq

description:
fragmentented two times Poly(A) selected ds_cDNA
Sample 24


title: AR_Cast+T_rep1b [prostate, castrated+testosterone]

tag: strain

value: prostate

tag: age

value: castrated+testosterone

value: AR (Sahu et al. 2011)


title: Mouse_ESCs_MLL2-/-_4d_atRA_H3K4me3

description: Sample 13

tag: genotype/variation

value: atRA for 4 days


title: Mouse_ESCs_MLL1-/-_4d_atRA_H3K4me3

description: Sample 12

value: Embryonic Stem Cells (ESCs)


title: Mouse_ESCs_MLL2_F/F_H3K4me3

description: Sample 10


title: E14_Ash2L_GFP

data_processing:
Initial data processing, base calling, and alignment to the mouse reference genome was performed using the Illumina Analysis Pipeline allowing one mismatch. Only tags aligning to one position on the genome were considered for further analysis.
For this ChIP-Seq, the uniquely mapped sequence reads were directionally extended to 200 bp, the estimated median length of the original DNA library. If multiple tags mapped on the same genomic position, only one was included for further analysis.
The ChIP-Seq data was converted to Browser Extensible Data (BED) files for downstream analysis. To compensate for differences in sequencing depth and mapping efficiency among samples, the total number of unique reads of each sample was uniformly equalized relative to the sample with the lowest number of sequence reads, allowing quantitative comparisons.
Wiggle (WIG) files for viewing the data in the UCSC Genome Browser were generated from the normalized files.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated according to general instructions and were used for analysis; Wig files can be directly uploaded to the UCSC genome browser.

source_name: Embryonic Stem Cells

growth_protocol: ES cells were cultured without feeders in the presence of leukemia inhibitory factor (LIF) either in Glasgow modification of Eagles medium (GMEM) containing 10% fetal calf serum

extract_protocol:
Experiments were performed with 3.3 million cells and 3 microgram antibody per ChIP. Crosslinking was performed on the culture plates for 20 min and ChIP’ed DNA was purified by Qiaquick PCR purification Kit (QIAGEN).
DNA samples from ChIP-Seq were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Integrity of DNA libraries was confirmed by running the products on a Bioanalyzer (BioRad). Cluster generation and sequencing (36 bp) was performed with the Illumina Genome Analyzer IIx (GAIIx) sequencing platform according to standard Illumina protocols.

value: containing Ash2L_GFP

value: Custom GFP antibody

tag: chip antibody info.

value: MPI-CBG 'anti-GFP 2007' (Vermeulen et al., 2010)


title: Mouse_ESCs_MLL1&MLL2_FC/FC_H3K4me3

description: Sample 9


title: E14_empty_GFP

value: wild type


title: Mouse_ESCs_MLL1-/-_H3K4me3

description: Sample 7


title: E14_MLL2_N_GFP

value: containing MLL2_N_GFP


title: E14_Cxxc1_GFP

value: containing Cxxc1_GFP


title: E14_PolII

description: Sample 21

value: Antibody RNA Pol II


title: MLL2KO_H3K4me3

tag: chip antibody lot. #


title: Intermediate-size Non-coding RNA

first: Xuncheng

address: 5 Yiheyuan Road

institute: Peiking University

data_processing:
The validated reads were mapped to Arabidopsis genome TAIR10, and all overlapping reads were collected as separate loci. Subsequently, tRNA and rRNA related loci were discarded using tRNAscan program (Lowe and Eddy, 1997) and a homology comparison of the rRNA sequences was performed according to the TAIR annotation. Then, the consensus sequences and the sequence termini of each reads-merging locus were obtained from multiple-reads alignment. The consensus sequences retained as distinct ncRNAs were remapped to Arabidopsis genome to determine the non-coding loci across the whole genome. Only the best matches were considered as putative ncRNAs. Furthermore, small nucleolar RNAs (snoRNA) were identified based on their conserved motifs and secondary structures (Chen et al., 2003; Matera et al., 2007). The sequences with 5’ end box C (RUGAUGA), 3’ end box D (CUGA), and terminal short inverted repeats were identified as box C/D snoRNA candidates. The sequences exhibiting a typical hairpin-hinge-hairpin-tail secondary structure, with box H (ANANNA) in the hinge region and box ACA from the end of sequence were identified as box H/ACA snoRNA candidates. Program M-fold in Linux was employed to predict the secondary structures of each consensus sequence (Zuker, 2003). MicroRNAs were annotated according to miRBase (Griffiths-Jones et al., 2008) annotation. Other ncRNAs were annotated by homology comparison in NONCODE 2.0 (He et al., 2008), Rfam 9.1 (Gardner et al., 2009) and NCBI.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file include read numbers for each identified non-coding RNA loci

organism: Arabidopsis thaliana

source_name: whole plant

extract_protocol:
total RNA was isolated  and the im-ncRNAs were enriched by anion column-based size selection (50~300nt). Abundant small ribosomal RNAs were removed from total RNAs upon hybridization to designed probes, resulting in a pool of enriched im-ncRNAs. In libraries to separate 5’-capped and 5’-phosphate ncRNAs, total small ncRNAs were de-phosphated with Alkaline Phosphatase (AP) and ligated to 3’ adaptor (3AD). The ligated products were treated with PolyNucleotide Kinase (PNK), ligated to a 5’ adaptor (5AD-GS1) and again treated with AP to remove un-ligated free 5’ end phosphate. Then the cap structures (if any) were removed from capped ncRNAs by Tobacco Acid Phosphatase (TAP) and ligated to another 5’ adaptor (5AD-GS2). In libraries to separate 5’ mono- and triple- phosphate ncRNAs, im-ncRNAs were first ligated to excessive 5AD-GS1, followed by 3AD-GS ligation. Then the tri-phophate ncRNA were converted to mono-phosphate by treatments of AP and PNK, consequently, and ligated to 5AD-GS2
im-ncRNAs flanked by adaptors at both ends were reverse transcribed with the primer 3RT-GS and purified, resulting in single-stranded cDNA library. The adaptors are designed to be compatible with the 19nt primers A and B of 454 sequencing (Margulies et al., 2005)

value: root, whole seedling, stem, rosette leave, flower/inflorescence, and silique


title: E14_H3K4me3


title: E14_Mll2FL_C_GFP_FCS_LIF_2i_double_crosslink

description: Sample 29

value: containing MLL2_C_GFP

value: Custom GFP antibody from MPI-CBG "anti-GFP 2007" (Vermeulen et al., 2010)


title: E14_mock_GFP_FCS_LIF_2i_double_crosslink

description: Sample 30

value: wildtype


title: E14_Mll2FL_N_GFP_FCS_LIF_2i

description: Sample 28


title: adr1 dsRBD mutant

city: La Jolla

first: Boyko

last: Kakaradov

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

description: RNA extracted by Trizol reagent and isolated with cloroform.

data_processing:
ssRNAseq: The adr-1(-);adr-2(-) sample was sequenced on one lane of Illumina's HiSeq 2000 yielding 216 million single-end 76nt reads.  Each other sample was sequenced on a lane of Illumina GAII yielding between 37 and 42 million reads of the same type.  Illumina Casava1.8.2 software used for basecalling.
Mapping: Sequenced reads were mapped to the C. elegans reference genome (ce10) using TopHat aligner (version 2.0.6) allowing only uniquely-mapped reads with up to two mismatches each with command line options -Mx 1 and -N 2
Variant calling: sites with RNA-DNA differences were identified by SAMtools mpileup (version 0.1.18) tallying up to 1000 alignments per site.  Additional command line options used were -D -I and -g.
Site filters: Annotated SNPs were obtained from Illumina's iGenomes collection for C. elegans (ce10) and unannotated variants were extracted from the adr-1(-);adr-2(-) RNA-Seq dataset.  These genomic variants were filtered from the putative sites in all other strains reducing the number of false-positive predictions.
Read filters:  Each read aligned to one the remaining putative sites was filtered out if: a) it was a suspected PCR duplicate, according to SAMtools rmdup (version 0.1.18); b) it had a junction overhang < 10nt according to its SAMtools CIGAR string; c) it had > 1 non-A2G or non-C2T mismatch or any short indel, per its MD tag; d) it had a mismatch less than 25nt away from either end of the read
Identify sites:  Putative RNA editing sites were identified from A2G variants on the sense strand and T2C variants on the antisense strand that were covered by more than 5 reads which passed the filters in step 5, including the stringent 25nt threshold for filter 5d).
Quantify sites: The extent of editing at each site and our confidence in that prediction were quantified by a novel extension of the classical Bayesian model used for genomic variants, which is described in more detail in the next section.
To increase the accuracy and confidence of our predictions, we used additional reads from the relaxed version of filter 5d) that overlap the sites identified in step 6.  Moreover, we dropped sites that exhibited editing in 100% of the reads (suggesting a genomic variant not filtered out by step 4) and those with very low editing (less than 10%), which would have been hard to distinguish from sequencing errors.
The predicted RNA editing sites from each strain were characterized according to their position in annotated genic regions (introns, exons, 3'/5' UTRs, etc.) and according to their overlap with other strains.
Supplementary_files_format_and_content: tab-delimited text file containing #READS and %EDITING values for each editing site
Genome_build: ce10

organism: Caenorhabditis elegans

source_name: BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD1 (K223E, K224A, and K227A)]

growth_protocol: Transgenic worm lines were generated by microinjection into the gonads of young adult worms of the appropriate genetic background

extract_protocol:
Total RNA was extracted using Trizol reagent.
RNA libraries were prepared for strand specific RNA sequencing using the published protocol (Parkhomchuk et al. Nucleic Acid Research. 2009 37(18):e123)

treatment_protocol: The injection mix used for generating transgenics contained the following: 1ng/μl of the transgene of interest, 20ng/μl of the dominant marker, and 79ng/μl of 1kb DNA ladder (NEB)

value: whole worms

tag: genetic background


title: FLAG ADR1- rescue

source_name: BB21 adr-1(tm668) + blmEx1[ 3XFLAG-adr-1 genomic, rab3::gfp::unc-54]

tag: genotype


title: adr1/adr2 double mutant

source_name: BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD1 (K223E, K224A, and K227A) and dsRBD2 (K583E, K584A and K587A)]


title: hsa ov F1 [batch1]

status: Public on Jan 19 2014

city: Lyon

first: Anamaria

last: Necsulea

address: 43 Bd. du 11 Novembre 1918

department: Laboratoire de Biométrie et Biologie Evolutive

institute: CNRS, Université Claude Bernard Lyon 1

description: This sample had unusual expression patterns (absence of Xist, presence of Y-specific transcripts). We removed it from expression analyses, but we used it in the pools of samples for lncRNA detection.

data_processing:
The basecalling was performed with the Illumina GAIIx pipeline, version 1.8  and with Ibis (Kircher et al, 2009). Ibis was used on non-strand specific samples and on hsa br M 2ss.. The quality values are given in the phred-33 format, for all samples.
Raw reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
Splice junctions were detected from TopHat unambiguous read alignments, requiring an anchor size of at least 8bp and at most 1 mismatch per alignment.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks.Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type ${librarytype} --multi-read-correct. For strand-specific samples, the library-type was set at fr-secondstrand (batch 1) or fr-firststrand (batch 2), while for non-strand-specific samples the library-type was set at fr-unstranded. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Genome_build: hg19, gorGor3, MMUL_1, mm9, monDom5, ornAna1, galGal3, JGI 4.2
Supplementary_files_format_and_content: .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated. .bedGraph files contain genome-wide read coverage statistics, in bedGraph format, obtained with the "wiggles" utility in TopHat.

source_name: Ovary

extract_protocol:
Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Non-strand-specific sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer's instructions. Briefly, polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded cDNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 250-300 bp fragments were excised and then PCR-amplified (15 cycles). After column-purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalyzers. Strand-specific libraries were prepared using an optimized version of the original Directional mRNA-seq Library Prep Pre-Release Protocol from Illumina. We used reagents from various companies instead of Illumina’s to decrease significantly the library cost and as a consequence adapted the reaction parameters for each step. In addition, we integrated a size selection step, right after fragmentation to optimize the insert size distribution and decrease the adapter contamination. This optimized protocol is available upon request.

tag: Sex

value: female

value: adult, 47 years

value: Illumina GAIIx, strand-specific

tag: library-type (for tophat and cufflinks)

value: fr-secondstrand


title: adr1-/adr2- double knockout


title: adr1- knockout worms


title: Mouse_ESCs_MLL2_FC/FC_H3K4me3

description: Sample 8

value: induced Mll2 -/-

value: Embryonic Stem Cells (ESCs)

tag: chip antibody

value: Diagenode


title: hsa ts M3 [batch1]

source_name: Testis

value: male

value: adult, 51 years


title: adr2 dsRBD mutant

source_name: BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD2 (K583E, K584A and K587A)]


title: hsa pl M1 [batch1]

source_name: Placenta

value: embryo, 13 weeks post-conception


title: N2 wild type worms

source_name: Bristol strain N2

value: wild type


title: adr2- knockout worms


title: hsa br M7 [batch1]

source_name: Brain, frontal cortex

value: adult


title: hsa br M 2ss [batch1]

value: adult, 48 years


title: mml ts M 1 [batch1]

description: Additional coverage for GSM752642.

organism: Macaca mulatta

value: adult, 8 years

value: Illumina GAIIx, non-strand-specific

tag: library-type (for tophat or cufflinks)

value: fr-unstranded


title: FoxA1_ChIP Seq

description: Sample 3

tag: cell line

value: androgen-dependent prostate cancer derived cell line LNCaP

tag: passage number

value: FoxA1 [Abcam 23738]

value: control


title: hsa br M 9 [batch2]

description: polyA RNA

data_processing:
The basecalling was performed with the Illumina GAIIx pipeline, version 1.8, as well as with the Illumina HiSeq 2000 pipeline  and with Ibis (Kircher et al, 2009). Ibis was used on non-strand specific samples generated with Illumina GAII. The quality values are given in the phred-33 format, for all samples.
Raw reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
Splice junctions were detected from TopHat unambiguous read alignments, requiring an anchor size of at least 8bp and at most 1 mismatch per alignment.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks.Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type ${librarytype} --multi-read-correct. For strand-specific samples, the library-type was set at fr-secondstrand (batch 1) or fr-firststrand (batch 2), while for non-strand-specific samples the library-type was set at fr-unstranded. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Paired-end RNA-seq samples were treated as single-end for comparability, i.e. only the first read of the pair was used for expression analyses.
Small RNA-seq reads were trimmed to remove adapter sequences. We kept reads with trimmed sizes between 15 and 25 bp, which are compatible with mature miRNA sizes. The trimmed reads were mapped on the Ensembl 62 miRNA precursors, using Bowtie.  miRNA expression levels were computed as the number of reads that mapped uniquely to each Ensembl-annotated miRNA precursor.
Genome_build: hg19, mm9, monDom5, ornAna1, galGal3, JGI 4.2
Supplementary_files_format_and_content: The .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated.
Supplementary_files_format_and_content: The .bedgraph files contain genome-wide read coverage statistics, obtained with the "wiggles" utility in TopHat.
Supplementary_files_format_and_content: For miRNA data, the .txt files contain the number of reads (unique and total) that could be assigned to a given miRNA precursor annotated in Ensembl. Reads that aligned to more than 1 Ensembl-annotated miRNA precursor were "divided" equally among the different precursors; thus, the "total" number of reads is not necessarily an integer.

extract_protocol:
Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Non-strand-specific sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer's instructions. Briefly, polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded cDNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 250-300 bp fragments were excised and then PCR-amplified (15 cycles). After column-purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalyzers.
Strand-specific libraries were prepared using an optimized version of the original Directional mRNA-seq Library Prep Pre-Release Protocol from Illumina. We used reagents from various companies instead of Illumina’s to decrease significantly the library cost and as a consequence adapted the reaction parameters for each step. In addition, we integrated a size selection step, right after fragmentation to optimize the insert size distribution and decrease the adapter contamination. This optimized protocol is available upon request.

value: Illumina GAII, non strand-specific


title: hsa br M 10 [batch2]

description: polyA RNA


title: oan br M2 [batch1]

organism: Ornithorhynchus anatinus

source_name: Brain

value: Illumina GAIIx, strand-specific

value: fr-secondstrand


title: oan ov F1 [batch1]

data_processing:
The basecalling was performed with the Illumina GAIIx pipeline, version 1.8  and with Ibis (Kircher et al, 2009). Ibis was used on non-strand specific samples and on hsa br M 2ss.. The quality values are given in the phred-33 format, for all samples.
Raw reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
Splice junctions were detected from TopHat unambiguous read alignments, requiring an anchor size of at least 8bp and at most 1 mismatch per alignment.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks.Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type ${librarytype} --multi-read-correct. For strand-specific samples, the library-type was set at fr-secondstrand (batch 1) or fr-firststrand (batch 2), while for non-strand-specific samples the library-type was set at fr-unstranded. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Genome_build: hg19, gorGor3, MMUL_1, mm9, monDom5, ornAna1, galGal3, JGI 4.2
Supplementary_files_format_and_content: .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated. .bedGraph files contain genome-wide read coverage statistics, in bedGraph format, obtained with the "wiggles" utility in TopHat.
Please note that this sample is identical to GSM881436 (however, different processed data is provided here).

extract_protocol:
Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Non-strand-specific sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer's instructions. Briefly, polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded cDNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 250-300 bp fragments were excised and then PCR-amplified (15 cycles). After column-purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalyzers. Strand-specific libraries were prepared using an optimized version of the original Directional mRNA-seq Library Prep Pre-Release Protocol from Illumina. We used reagents from various companies instead of Illumina’s to decrease significantly the library cost and as a consequence adapted the reaction parameters for each step. In addition, we integrated a size selection step, right after fragmentation to optimize the insert size distribution and decrease the adapter contamination. This optimized protocol is available upon request.
Please note that this sample is identical to GSM881436 (however, different processed data is provided here).

value: female


title: hsa br M 8 [batch2]

description: polyA RNA


title: xtr ts M1 [batch1]

organism: Xenopus tropicalis

value: adult (4-6 months)


title: oan ts M4 [batch1]

value: male


title: xtr ov F1 [batch1]


title: xtr lv F1 [batch1]

data_processing:
The basecalling was performed with the Illumina GAIIx pipeline, version 1.8  and with Ibis (Kircher et al, 2009). Ibis was used on non-strand specific samples and on hsa br M 2ss. The quality values are given in the phred-33 format, for all samples.
Raw reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
Splice junctions were detected from TopHat unambiguous read alignments, requiring an anchor size of at least 8bp and at most 1 mismatch per alignment.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks.Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type ${librarytype} --multi-read-correct. For strand-specific samples, the library-type was set at fr-secondstrand (batch 1) or fr-firststrand (batch 2), while for non-strand-specific samples the library-type was set at fr-unstranded. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Genome_build: hg19, gorGor3, MMUL_1, mm9, monDom5, ornAna1, galGal3, JGI 4.2
Supplementary_files_format_and_content: .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated. .bedGraph files contain genome-wide read coverage statistics, in bedGraph format, obtained with the "wiggles" utility in TopHat.

source_name: Liver


title: xtr kd F1 [batch1]

source_name: Kidney


title: xtr ht F1 [batch1]

source_name: Heart


title: mml br M 1 [batch1]

description: Additional coverage for GSM752632.


title: xtr ht M1 [batch1]


title: mmu pl F1 [batch1]

value: embryo, 16.5 days post-conception


title: mdo pl I1 [batch1]

organism: Monodelphis domestica

value: unknown

value: embryo, 13 days post-conception


title: mdo br M2 [batch1]

value: adult, 13 months


title: xtr br F1 [batch1]


title: xtr br M1 [batch1]


title: mdo ov F1 [batch1]

value: adult, 20 months


title: DNase_mES_Day6_Prepancreatic_Endoderm

city: Cambridge

first: David

last: Gifford

state: MA

address: 32 Vassar Street

department: Electrical Engineering and Computer Science

institute: Massachusetts Institute of Technology

data_processing:
Illumina Casava 1.8 processing was used and reads were saved into FASTQ files using the standard 33 offset in ASCII Qscore encoding.
Sequenced reads were directly mapped to mm10 genome using BWA version 0.6.2 with default parameters.
Non-unique and low quality reads (MAPQ<20) were removed before normalization and analysis by the PIQ algorithm.
For each sample PIQ input mapped reads from a BAM file, a list of TF sequence PWMs, and produced a text file indicating putative TF binding sites per PWM. Only those PWMs found to exhibit a significant DNase I profile were included (significance threshold: >100 of the 399 bases within the profile passing 5% FDR).
Genome_build: mm10
Supplementary_files_format_and_content: PIQ output: one text file for each sample indicating putative TF binding sites. These files contain the following columns: Chromosome, TF motif center (beginning), TF motif center (end; equal to prior column if motif has odd length), TF identifier, PWM/Sequence match score, direction of PWM match, and PIQ TF binding score

source_name: Murine Prepancreatic Endoderm Cells

growth_protocol: Mouse embryonic stem cell culture and endoderm differentiation was modified slightly from previously published protocols (Sherwood, et al., Mech. Dev. 2011). Undifferentiated 129P2/OlaHsd mESCs were maintained on gelatin-coated plates with mouse embryonic fibroblast (MEF) feeders in mESC medium composed of Knockout DMEM (Life Technologies) supplemented with 15% defined FBS (HyClone), 0.1 mM nonessential amino acids (Life Technologies), 1% Glutamax (Life Technologies), 0.55 mM 2-mercaptoethanol (Sigma) and 1x ESGRO LIF (Millipore). Before differentiation, ESCs were passaged onto gelatin-coated plates for 25 min to deplete MEFs. MEF-depleted ESCs were then seeded at 1x104 cells/cm2 onto gelatin-coated dishes in mESC medium. After 12–24 h, medium was changed to Advanced DMEM (Life Technologies) supplemented with N-2 (Life Technologies), B27 without vitamin A (Life Technologies) and 1% Glutamax. After 44–48 h, medium was changed to Advanced DMEM with 2% FBS, 1% Glutamax, 5 nM GSK-3 inhibitor XV and 50 ng/ml Escherichia coli–derived Activin A (Peprotech) for 24 h to produce mesendoderm. For endoderm differentiation, cells were then fed with Advanced DMEM with 2% FBS, 1% Glutamax, 50 ng/ml Activin A and 1 μM dorsomorphin (Sigma) for 48 h. For intestinal endoderm differentiation, cells at the endoderm stage were fed for 24 h with Advanced DMEM with B-27 supplement without vitamin A, 1% Glutamax and 100 nM GSK-3 inhibitor XV. For differentiation of prepancreatic endoderm, cells at the endoderm stage were fed for 24 h with Advanced DMEM with B-27 supplement without vitamin A, 1% Glutamax, 500 nM retinoic acid (Calbiochem), 50 nM A-83-01 (Calbiochem) and 8 ng/ml Bmp4 (Stemgent). For mesodermal differentiation, cells at the mesendoderm stage were treated for 48 h with 10 ng/ml Bmp4.

extract_protocol:
Samples prepared into Illumina libraries using the Beckman Coulter Genomics SPRI-works system using custom adapters. 6nt 3’ barcodes were added during PCR enrichment and the resulting fragments were evaluated using Agilent BioAnalyzer 2100.   Samples were sequenced one-per-lane using an Illumina HiSeq 2000.
Libraries were diluted to 10nM and then run on qPCR with p5 and p7 primers to determine final flow cell loading concentration, normalized to a PhiX control library. PhiX spike: Each lane was spiked with approximately 0.25-0.5% PhiX control library. Samples were run one-per-lane using Standard Illumina protocols using the following: TruSeq SR/PE Cluster kit V3 cBot, TruSeq SBS Reagent Kit V3, RTA version 1.12.4.2, and Control software version 1.4.8.

treatment_protocol:
DNase-Seq was performed using adaptations of previous protocols (Sekiya, et al., Genes Dev. 2009). 1-3 biological replicate DNase-Seq experiments were performed at six stages of mouse ES cell differentiation: mouse ES cells, mesendoderm, endoderm, lateral plate mesoderm, pre-pancreatic endoderm, and intestinal endoderm. A detailed protocol is as follows:
Mouse ES cells or differentiated cells of various stages (30-90 million cells) were harvested from 15 cm tissue culture plates, pelleted at 800g for 5 minutes at 4°C and the supernatant aspirated. Cells were washed twice with 2.5 ml/plate of ice-cold PBS and pelleted (800g, 5 minutes, 4°C). The supernatant was aspirated and cells were resuspended 2.5 mL/plate Buffer A containing 15 mM Tris HCl (pH 8), 15 mM NaCl, 60 mM KCl, 1 mM EDTA (Ambion, pH 8), 0.5 mM EGTA (pH 8) and 0.5 mM Spermidine (Sigma-Aldrich). An equal volume of 2X Igepal in Buffer A (earlier samples with a 0.05% Igepal final concentration, later samples with a 0.00165% Igepal final concentration) was added to the resuspended cells and the nuclei were pelleted (800g, 5 minutes, 4°C). The supernatant was aspirated promptly and the cells resuspended in 2.5 mL/plate Buffer A. An aliquot of the resuspended nuclei was taken and counted on a hematocytometer with 1:10 Trypan Blue. Nuclei were pelleted (800g, 5 minutes, 4°C) and either digested immediately as below, or stored in 20 mM Tris HCl (pH 8), 75 mM NaCl, 0.5 mM EDTA (Ambion) 50% glycerol, 0.85 mM DTT, and 0.125 mM PMSF, flash frozen in liquid nitrogen and stored at -80°C for a later digestion.
If frozen, nuclei were washed twice with 2.5 mL/plate Buffer A, pelleted (800g, 5 minutes, 4°C) and the supernatant discarded before proceeding to digestion. Digestion volumes are given for 107 nuclei.  Volumes should be scaled as per cell number. Digestion buffer (850 μl per 107 nuclei) was prepared by diluting 10X stock of CaCl2 and NaCl in Buffer A (above) for a final concentration of 6 mM CaCl2 and 75 mM NaCl. Stop buffer (950 μl  per 107 nuclei) was prepared with final concentrations as follows: 50 mM Tris HCl (pH 8), 100 mM Na Cl, 0.1 % SDS, 100 mM EDTA (Ambion, pH 8), 10 μg/ml RNase A (Invitrogen), 1 mM Spermidine (Sigma-Aldrich) and 0.5 M Spermine (Sigma-Aldrich). Both digestion and stop buffers were warmed at 37°C. DNase I enzyme was combined with warmed digestion buffer for a final volume of 100 μl per 107 nuclei. If multiple concentrations of DNase I were tested, nuclei were separated equally amongst each concentration. Prior to digestion, a small aliquot was reserved as an undigested control for quantitative PCR analysis. The DNaseI/ digestion buffer mix was warmed in a 37°C water bath for 2 minutes, and the nuclei were gently resuspended in digestion buffer. The warmed DNaseI/ digestion buffer mix was promptly added to the nuclei and digested for 2 minutes at 37°C. Pre-warmed stop buffer was added and the tube inverted multiple times to stop the digestion. Digested samples were transferred to a 55°C incubator for 15 minutes. Proteinase K (Ambion, 20 mg/mL) was added to each sample for a final concentration of 2μg/mL and samples were incubated overnight at 55°C.
DNA fragments were purified by adding an equal volume of phenol:chloroform:isoamyl alcohol to each sample and mixing. The suspension was transferred to a phase-lock tube and centrifuged for 5 minutes at 12-16,000g. The aqueous phase was isolated and combined with 0.1 volumes 3M sodium acetate, 2 volumes absolute ethanol and 1:600 Glycoblue. This mixture was incubated at -20°C for 5-6 hours or at -80°C for 30-45 minutes. DNA was pelleted by centrifugation at 12-16000g for 10-20 minutes and the supernatant aspirated. The DNA pellet was washed with 70% ethanol and re-pelleted by centrifugation at 4000 rpm for 5 minutes. The supernatant was carefully aspirated and the DNA pellet air-dried for 5-10 minutes before resuspending in TE buffer.
To enrich for hypersensitive regions, size selection was performed on the purified fragments by either 2% agarose gel band purification or the Invitrogen E-Gel Agarose System. Fragments were collected in the 175-400 bp region so as to avoid empirically-determined complications by the ~150 bp nucleosomal signal. Size selection enrichment was tested by quantitative PCR using primers (three positive control primers and three negative control primers) for constitutively DNase hypersensitive regions and insensitive regions as positive and negative controls respectively, on both the samples as well as the reserved undigested controls. Size selection enrichment was calculated as follows: Enrichment = 2^((Ct(negative control primer)-Ct(positive control primers))digested, size selected fragments-(Ct(negative control primer)-Ct(positive control primers))undigested control).

tag: cell type

value: mESC-derived Prepancretic Endoderm Cells

tag: datatype

value: DNase-seq

tag: cell sex

value: F


title: DNase_mES_Day5_Endoderm

source_name: Murine Endoderm Cells

value: mESC-derived Endoderm Cells


title: DNase_mES_Day6_Intestinal_Endoderm

source_name: Murine Intestinal Endoderm Cells

value: mESC-derived Intestinal Endoderm Cells


title: mmu ov F1 [batch1]

data_processing:
The basecalling was performed with the Illumina GAIIx pipeline, version 1.8  and with Ibis (Kircher et al, 2009). Ibis was used on non-strand specific samples and on hsa br M 2ss.. The quality values are given in the phred-33 format, for all samples.
Raw reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
Splice junctions were detected from TopHat unambiguous read alignments, requiring an anchor size of at least 8bp and at most 1 mismatch per alignment.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks.Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type ${librarytype} --multi-read-correct. For strand-specific samples, the library-type was set at fr-secondstrand  (batch 1) or fr-firststrand (batch 2), while for non-strand-specific samples the library-type was set at fr-unstranded. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Genome_build: hg19, gorGor3, MMUL_1, mm9, monDom5, ornAna1, galGal3, JGI 4.2
Supplementary_files_format_and_content: .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated. .bedGraph files contain genome-wide read coverage statistics, in bedGraph format, obtained with the "wiggles" utility in TopHat.

value: adult


title: mmu br M4 [batch1]


title: DNase_mES_Day5_Mesoderm

source_name: Murine Mesoderm Cells

value: mESC-derived Mesoderm Cells