title: Pol2_IP_rtt109_2

first: Craig

middle: L

last: Peterson

state: MASSACHUSETTS

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: Immunoprecipitated DNA

data_processing:
Fastq files were put through the FASTQC program to verify good quality of library
alignment to the sacCer3 genome using Bowtie2 to obtain SAM files. SAMtools was used for SAM to BAM conversion with the FLAGs to discard PCR duplicates and multiple mapping reads.
Each sample was normalized to total library read count (bamCoverage tool in the deepTools package)
After determining strong correlation values, the replicates were summed for further analysis.
IP/Input ratios: Every base of the genome was assigned the total number of sequence reads overlapping it, separately for the input and IP sequence reads. Subsequent normalization and analysis was performed on median read coverage across 100-bp windows, sliding along each chromosome in 50-bp steps. The median IP coverage of each 100-bp interval was divided by the median input coverage for the same window. The IP/input ratios of each interval were normalized, dividing by the median genome- wide IP/input. Positions with fewer than 20 input reads were excluded from all subsequent analysis because of unreliable enrichment associated with division by low numbers.
Genome_build: sacCer3
Supplementary_files_format_and_content: bed files were generated using BEDTools and represent the IP/input ratio in 100bp window, sliding along the chromosome in 50bp steps individually for each mutant, replicates combined. BED files are available on the series record.

source_name: Budding yeast cells

growth_protocol: Yeast were grown in Yeast Extract Peptone (YEP) media (100ml per IP) with 2% glucose at 30°C

extract_protocol:
Cell lysis by bead beating (6 cycles of 1 min each) and chromatin fragmentation with 200 units of Mnase at 37˚C. Clarified lysates were IPed with Anti-CTD overnight and followed by incremental salt washes, and phenol chloroform extraction to isolate the IP DNA
Standard BGI protocol was used as follows: i) quality control by Qubit and Agilent 2100 ii) Addition of A base to 3’ end and adapter ligation iii) PCR amplification and size selection for 100-300 bp and, finally iv) Library QC by Agilent 2100 and qPCR.

treatment_protocol: Cells were crosslinked with 1% formaldehye at room temperature for 20 min, quenched with glycine and processed for IP

tag: cell density

value: Log phase (OD= 0.8)

tag: cell cycle stage

value: Asynchronous

value: 6ul of Anti-CTD (8WG16 Covance)


title: E. coli Dam- IP

status: Public on Nov 12 2015

type: SRA

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
DIP-Seq
All reads were trimmed using sickle and the fastx toolkit (removing bases with <Q20).
M. musculus reads were mapped to mm9 with variations as in publication using bwa 0.6.2
X. laevis reads were mapped to LAEVIS7.1 with variaitions as in publication using bwa 0.6.2
E. coli reads were mapped to the K12 genome (NCBI Reference NC_000913.2) using bwa 0.6.2
bigwigs were generated by extending the reads to 300 bases and binned to 50 bases.
Genome_build: E.coli NC_000913.2; mm9;
X. laevis 7.1 at ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla7.1/
Supplementary_files_format_and_content: bigwigs - binned tracks for visualisation

molecule: genomic DNA

organism: Escherichia coli

source_name: E. coli Dam- IP

growth_protocol: Freshly isolated tissue was used

extract_protocol:
genomic DNA was extracted using Phenol and Quiagen Dneasy Blood and Tissue Kit
Libraries were prepared accroding to Ford et al (BMC Res. Notes 7, 312, 2014). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12-18 cycles and library fragments of 250-350 bp ) were band isolated with Agencourt beads. 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.

tag: strain

tag: strain info

value: Dam- bacteria

tag: antibody

value: m6A (N6-methyladenosine)

tag: antibody vendor

value: Synaptic Systems GmbH

tag: cat. #


title: Input_DNA

city: Worcester

country: USA

description: Input DNA

organism: Saccharomyces cerevisiae

tag: chip antibody

value: none (input)


title: Pol2_IP_rtt109_1

description: Immunoprecipitated DNA


title: Pol2_IP_rrp6_2

description: Immunoprecipitated DNA


title: ribosome profiling

city: Aurora

first: Neelanjan

last: Mukherjee

state: CO

department: BMG/RBI

institute: University of Colorado School of Medicine

library_source: transcriptomic

data_processing:
Reads aligning to rRNA sequences were discarded using Bowtie (v1.00), with the following parameters: "--best"
Unaligned Ribo-seq reads and RNA-seq reads were aligned to the human genome (hg 19) using the split-aware aligner STAR (v2.3.1z1). The STAR genome index was built using annotation obtained from GENCODE (version 19). A maximum of 4 mismatches were allowed and multi-mapping to up to 8 different position was permitted.  Parameters " --alignEndsType EndToEnd --outFilterMismatchNmax 4 --outFilterMultimapNmax 8 --chimScoreSeparation 10 --chimScoreMin 20 --chimSegmentMin 15 --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignSJoverhangMin 500 "
Alignments flagged as secondary alignment were filtered out with samtools (v0.1.18), ensuring 1 genomic position per aligned read. "samtools view -b -F 0X100"
RiboTaper was applied to find ORFs and quantify the p-site positions per ORF (reported in score column of processed data bed file).
Genome_build: hg19
Supplementary_files_format_and_content: bed file of open reading frames determined by RiboTaper method

molecule: total RNA

organism: Homo sapiens

growth_protocol: HEK293 Flip-In T-REx cells containing a FLAG-HA-tagged GFP were cultured in DMEM supplemented with 10% tet-reduced FBS and appropriate selection antibiotics.

extract_protocol:
For cell lysis, the cell medium was aspirated and cells washed with ice-cold PBS containing 100 µg/ml cycloheximide. No cycloheximide was added to the culture medium before. After thorough removal of the PBS, the plates were immersed in liquid nitrogen and placed on dried ice. For cell lysis, 400 µl mammalian polysome buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, with 1 mM DTT and 100 µg/ml cycloheximide added freshly) was supplied with 1% (v/v) Triton X-100 and 25 U/ml Turbo DNase (Life Technologies, AM2238) and dripped on the plate which is subsequently placed tilted on wet ice. The cells were scraped off to the lower portion of the dish so that they thawed in lysis buffer. After dispersal of the cells by pipetting, the lysate was triturated ten times through a 26G needle, cleared by centrifugation at 20000g for 5 minutes, flash-frozen in liquid nitrogen and stored at -80 °C until further usage. For isolation of ribosome-protected RNA fragments, 120 µl of the lysate were digested with 3 µl RNase I (Life Technologies, AM2294) for 45 min. at room temperature with rotation. The digestion was stopped by addition of 4 µl Superase-In (Life Technologies, AM2694). Meanwhile, MicroSpin S-400 HR columns (GE Healthcare, 27-5140-01) were equilibrated with 3 ml mammalian polysome buffer by gravity flow and emptied by centrifugation at 600g for four minutes. Of the digested lysate, 100 µl were then immediately loaded on the column and eluted by centrifugation at 600g for two minutes. RNA was extracted from the flow-through, approximately 125 µl, using Trizol LS (Life Technologies, 10296-010). Ribosomal RNA fragments were then removed using the RiboZero Kit (Illumina, MRZH11124) and separated on a 17% denaturing Urea-PAGE gel (National Diagnostics, EC-829).
The size range from 27nt to 30nt as defined by loading 20 pmol each Marker-27nt and Marker-30nt was cut out and the RNA fragments subjected to smallRNA library generation using 3'-Adapter NN-RA3, 5' adapter OR5-NN, RT primer RTP and PCR primers RP1 (forward primer) and RPI6-7 (reverse primer, containing barcodes). Libraries were sequenced on a HiSeq 2000 device (Illumina). After initial quality control, we obtained ~29 Mio raw reads by pooling the RPI6 and RPI7 samples.

tag: cell line


title: Pol2_IP_WT_1

description: Immunoprecipitated DNA


title: RNAseq-DKO-Preleukemic-2

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

description: RNA-seq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.9 with the standard parameters.
RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm).
Genome_build: mm9
Supplementary_files_format_and_content: 5hmc/5mc peaks in bed file; RNAseq gene expression value in cufflink fpkm_tracking file format

organism: Mus musculus

source_name: Preleukemic Cells

extract_protocol:
DNA was extracted by phenol/choloroform method.
RNA was isolated using Trizol.
5hmC enrichment was performed using a previously described procedure with an improved selective chemical labeling method (Song et al, Nature Biotechnology, 2011). DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25-50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. [Song, C.X., Szulwach, K.E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.H., Zhang, W., Jian, X., Wang, J., Zhang, L., Looney, T.J., Zhang, B., Godley, L.A., Hicks, L.M., Lahn, B.T., Jin, P., and He, C. (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nature Biotechnology, 29(1): 68-72.]
Enriched DNA from MeDIP were subjected to library construction using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina according the manufacturer’s protocol.
RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol.

tag: genotype/variation

value: DKO

tag: cell type

value: Preleukemic


title: M. musculus kidney IP replicate 3

source_name: M. musculus kidney IP

tag: gender

value: male

tag: developmental stage

value: adult

tag: tissue

value: kidney


title: Pol2_IP_WT_2

description: Immunoprecipitated DNA


title: GATA3_Th1_rep3

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

data_processing:
Reads were aligned to genome hg19 using Bowtie2 (technical replicates were merged at this step - L001 and L002), default settings
Peaks were called using MACS14 with the P-value cutoff of 10^-4
Genome_build: hg19

source_name: human naïve CD4+ T-cells  differentiated toward Th1 and Th2 until day 6

growth_protocol: Human naïve CD4+ T-cells were differentiated toward Th1 and Th2 until day 6. Naïve CD4+ T-cells were isolated from healthy donor buffy coats using a naïve CD4+ T-cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Naïve CD4+ T-cells were stimulated with plate-bound anti-CD3 (500 ng/mL) and soluble anti-CD28 (500 ng/mL) in the presence of IL-12 (5 ng/mL), IL-2 (10 ng/mL) and anti–IL-4 (5 µg/mL) for Th1, IL-4 (10 ng/mL), IL-2 (10 ng/mL), anti-IL-12 (5 µg/mL) and anti–IFN-g (5 µg/mL) for Th2.

extract_protocol:
To fix the DNA-protein complex, cells were cross-linked with 1/10 volume of cross-linking solution (50 mM HEPES-KOH [pH 7.5], 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 11% formaldehyde) for 10 min followed by quenching with 1/20 volume of 2.5 mM glycine solution for 10 min. Cells were harvested and washed twice with ice-cold PBS and pelleted, and nuclear fractions were prepared. The cell pellet was dissolved in 20 ml lysis buffer 1 (50 mM HEPES KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Nonidet P-40, and 0.25% Triton X-100 with protease inhibitor Complete Mini [Roche]) and incubated for 10min at 4°C followed by centrifugation at 2000 × g for 10 min at 4°C. The cell pellet was resuspended in 10 ml lysis buffer 2 (200 mM NaCl, 1 mM EDTA [pH 8], 0.5 mM EGTA, and 10 mM Tris [pH 8], with protease inhibitor) at room temperature for 10 min. Nuclei were pelleted at 2000 × g for 10 min at 4°C and resuspended in 1ml lysis buffer 3 (1 mM EDTA [pH 8], 0.5 mM EGTA [pH 8], and 10 mM Tris [pH 8], with protease inhibitor). The chromatin was sonicated for DNA fragmentation and analyzed with agarose gel electrophoresis. The majority of the DNA fragments were in the 500–100 bps range. Cell debris was pelleted by spinning at 10,000 × g for 10 min, and the supernatant was used for chromatin immunoprecipitation (ChIP). 20 μl chromatin supernatant was retained as the DNA input control. Sheep anti-rabbit IgG-conjugated Dynabeads (Dynal) were mixed with antibodies from commercial sources (α-GATA3, Santa Cruz sc-22206; α-MAF, Santa Cruz sc-10017X; α-MYB, Abcam ab45150) in blocking solution (PBS containing 5 mg/ml BSA) o/n at 4°C. Beads were collected and washed three times with PBS/BSA. Chromatin was equally divided into sample and control, adjusted with Triton-X-solution (0.1% Triton X-100, 0.1% sodium deoxycholate, and 1 mM PMSF) and mixed with magnetic beads pre-coated antibodies and incubated at 4°C o/n. Next day, magnetic beads were collected, put on magnetic stand and the supernatant was removed. Then beads were washed with 1 ml RIPA buffer (50 mM HEPES [pH 7.6], 1 mM EDTA, 0.7% sodium deoxycholate, 1% Nonidet P-40, and 0.5 M LiCl, with protease inhibitor mixture) at 4°C to remove nonspecific binding. The beads were collected and washed with RIPA buffer a total of 8-10 times. After washing once with 1 ml TE buffer, the beads were collected by centrifugation at 2000 × g for 2 min and resuspended in 50 μl elution buffer (50 mM Tris [pH 8], 10 mM EDTA, and 1% SDS). Chromatin was eluted from the beads by incubation at 65° for 30 min in a thermo-mixer followed by centrifugation for 1 min at 2000 × g. A total of 50 μl eluted supernatants were removed and mixed with 120 μl TE buffer. Similarly, 20 μl chromatin input control was mixed with 150 μl TE buffer. Decrosslinking was performed by incubation at 65°C overnight. Proteins in the DNA sample were digested in 120 μl proteinase K solution (2% glycogen, 5% proteinase K stock solution, and TE) for 2 h at 37°C. The DNA was then extracted twice with phenol and once with 24:1 chloroform/isoamyl alcohol. The sample was adjusted to 200 mM NaCl. After ethanol precipitation, the DNA was dissolved in 30 μl TE containing 10 μg DNase-free RNase A and incubated for 2 h at 37°C. The DNA was further purified with a Qiagen PCR kit (Qiagen).
Libraries for sequencing were generated as previously described in Hawkins et al, Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-491 (2010).

tag: biological replicate

tag: file identifier


title: GATA3_Th2_rep3


title: INPUT_Th1_rep1


title: INPUT_Th2_rep1


title: MAF_Th2_rep1


title: RNAseq-DKO-Preleukemic-1

description: RNA-seq


title: RNAseq-Tet2KO-LK-2

description: RNA-seq

source_name: LK Cells

value: Tet2 KO

value: LK


title: M. musculus kidney IP replicate 2


title: M. musculus kidney input replicate 3

source_name: M. musculus kidney input


title: M. musculus kidney IP replicate 1


title: MAF_Th1_rep2


title: M. musculus kidney input replicate 2


title: INPUT_Th1_rep2


title: MYB_Th1_rep2


title: MYB_Th1_rep1


title: MAF_Th1_rep1


title: MYB_Th2_rep1


title: Pol2_IP_rrp6_1

description: Immunoprecipitated DNA


title: M. musculus kidney input replicate 1


title: Input for SHP ChIP-seq with FGF19 treatment

city: Urbana

first: Jongsook

middle: Kim

last: Kemper

state: Illinois

address: 524 Burrill Hall  407 S. Goodwin Ave

department: Department of Molecular & Integrative Physiology

institute: University of Illinois at Champaign-Urbana

data_processing:
The libraries for ChIP-seq were sequenced with Illumina Genome Analyzer II. Basecalls were performed with CASAVA version 1.8.2.
The raw ChIP-seq reads were mapped to the mouse reference genome (UCSC mm9) with up to two mismatches using Bowtie 1 version 1.0.0 with options '–p 12 –S –v 2 –m 1 –t'.
Peaks were called by MACS2 version 2.0.10.20130501 using options '-g 1.87e9 -B'. Peaks with False Discovery Rate (FDR) < 0.05 were kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated by MACS2, score means the noramlized read coverage. Excel files include ChIP-seq peaks called by MACS2.

source_name: liver cell

extract_protocol:
Liver tissues were chopped by a razor blade and cross-linked in 1% (vol/vol) formaldehyde for 10 min at room temperature with rotation. Then, glycine to a concentration of 0.125 M was added to quench the cross-linking reaction. The chopped liver tissues were washed with ice-cold PBS and homogenized in hypotonic solution. Nuclei were isolated and chromatin DNA was sheared by sonication (Fisher Scientific, model 100). Four ug of SHP antibody (sc-30169, Santa Cruz) was added to the sheared chromatin and 10% of the sheared chromatin was saved for input. After incubation overnight at 4oC, protein G agarose beads were added and the incubation was continued for 1 h at 4°C with rotation. Then, the precipitated protein G agarose beads-antibody complex was washed by sodium- and lithium-chloride buffers. The input and the precipitated complexes were treated with RNase A and Proteinase K, and incubated at 65°C overnight to reverse crosslinks. DNA was isolated by phenol-chloroform extraction.
The ChIPseq libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit' with two modifications: adaptors were diluted 1:20 and adaptored DNAs were amplified for 15 cycles. The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane for 101 cyclesusing a TruSeq SBS sequencing kit version 3 and analyzed with Casava 1.8.2

treatment_protocol: Male C57BL6 mice (8-12 week old) were fasted for 12 h and injected via the tail vein with vehicle or FGF19 (1 mg/kg) at 9 a.m. Mice livers were collected 2 h after the treatment.

value: liver

tag: age

value: 8-12 week

tag: genotype

value: wildtype

tag: treatment


title: SHP ChIP-seq with FGF19 treatment

tag: strain


title: Sample 42: female whole-body x10

status: Public on Nov 11 2015

city: St. Andrews

first: David

last: Shuker

address: Greenside Place

department: School of Biology

institute: University of St Andrews

data_processing:
Reads were aligned to Nasonia Official Gene Set version 2 (OGS2, January 2012, http://arthropods.eugenes.org/EvidentialGene/nasonia/genes/) using GSNAP software v2013-02-05. Reads which mapped ambiguously, i.e. to more than one feature, were discarded.
Annotation and Gene Ontology information was obtained from the annotation for OGS2 generated by the Nasonia genome working group (http://www.hymenopteragenome.org/nasonia/?q=evidential_gene_data).
Read counts per sample were obtained using HTseq version 0.5.4p1 using “intersection-strict” mode whereby the whole read must map to a single transcript in order to be counted.
Because of the “intersection-strict” mode applied to HTSeq some of the reads which map ambiguously to a gene were removed and we were left with 155 799 857 reads which mapped to 20 388 genes.
Genome_build: Nasonia Official Gene Set version 2 (OGS2, January 2012, http://arthropods.eugenes.org/EvidentialGene/nasonia/genes/)
Supplementary_files_format_and_content: Single excel file containing read counts for each of the 42 samples for 20'388 features. Features are Identifiers from OGS2.

molecule: polyA RNA

organism: Nasonia vitripennis

source_name: female whole-body x10

growth_protocol: Focal females are "AsymC" strain. This highly inbred line was originally isolated in 1986. Wasps have been maintained on Calliphora vomitoria or C. vicina hosts at 25°, 16L : 8D light conditions ever since.

extract_protocol:
Focal females were pooled into groups of 10 and RNA was extracted from the whole bodies of these 10 individuals using the TRIzol Plus RNA purification system (Life Technologies, Paisley, UK).
Total RNA samples were prepared for sequencing using the illumina TruSeq RNA Sample Prep Kit (illumina, San Diego, CA, USA) following the illumina TruSeq Sample Preparation v2 (Low Sample) protocol. Briefly, mRNA molecules were purified from total RNA samples using oligo-dT attached magnetic beads and fragmented using divalent cations at 94 °C. First strand cDNA synthesis was carried out using reverse transcriptase and random hexamer primers. Second strand synthesis was carried out using RNA polymerase I and RNase H. Overhangs resulting from fragmentation were converted to blunt ends and 3’ ends were subsequently adenylated. Sanger indexing adapters were ligated to the fragments which were then purified and PCR-amplified to create the final cDNA libraries for sequencing. Libraries were sequenced on the HiSeq2000 according to the manufacturer’s instructions.

treatment_protocol: 2-day old mated females were given access to a single host for 24 hours to facilitate egg-development. This host was discarded and females were given access to honey solution for 24 hours. Following this females were alloted to the their treatment groups: isolated into glass vials and either left alone or with 9 red-eye mutant females. These two groups were then further subdivided and equal numbers were given no hosts, fres hosts or previously parasitised hosts.

tag: foundress number

tag: host type given

value: previously parasitised


title: Sample 41: female whole-body x10

value: fresh


title: SHP ChIP-seq with vehicle treatment

value: vehicle


title: Sample 40: female whole-body x10


title: Sample 38: female whole-body x10


title: Sample 37: female whole-body x10


title: Sample 39: female whole-body x10


title: Sample 36: female whole-body x10


title: Sample 33: female whole-body x10


title: Sample 35: female whole-body x10


title: Sample 34: female whole-body x10


title: Sample 29: female whole-body x10


title: Sample 32: female whole-body x10


title: Sample 31: female whole-body x10


title: Sample 30: female whole-body x10


title: Sample 28: female whole-body x10


title: Sample 27: female whole-body x10


title: Input for SHP ChIP-seq with vehicle treatment


title: Sample 22: female whole-body x10


title: Sample 23: female whole-body x10


title: Sample 21: female whole-body x10


title: Sample 24: female whole-body x10


title: Sample 18: female whole-body x10


title: Sample 25: female whole-body x10


title: Sample 15: female whole-body x10


title: Sample 16: female whole-body x10


title: Sample 17: female whole-body x10


title: Sample 26: female whole-body x10


title: Sample 19: female whole-body x10


title: Sample 14: female whole-body x10


title: Sample 12: female whole-body x10


title: Sample 13: female whole-body x10


title: Sample 10: female whole-body x10


title: Sample 9: female whole-body x10


title: Sample 5: female whole-body x10


title: Sample 11: female whole-body x10


title: Sample 8: female whole-body x10


title: Sample 7: female whole-body x10


title: male Offspring 3 (matBFMI)

city: Berlin

first: Gudrun

middle: A.

last: Brockmann

address: Invalidenstraße 42

department: Züchtungsbiologie und molekulare Tierzüchtung

country: Germany

institute: Humboldt-Universität zu Berlin

data_processing:
The standard illumina software pipeline was used for basecalling, after which a chastity filter was applied to remove low quality reads from the fastq files
Sequenced reads were trimmed for adaptor sequence (TruSeq3-PE-2.fa) using Trimmomatic v0.32 using the commaline arguments LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were then mapped to the mm10 whole genome fasta file using tophat v2.10 (which used bowtie2 v2.2.6) with parameters --prefilter-multihits --b2-sensitive --read-gap-length 12 --read-mismatches 2 --read-edit-dist 13 --max-insertion-length 20 --max-deletion-length 30
Picard tools v1.99 was used to mark optical duplicates,   The Genome Analysis Toolkit  v3.4.45 was used to perform Indel Realignment and  Base Recalibration using the mouse genome project v5 dbSNP-142 indels and snps as reference
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by merging exons from all isoforms of a gene to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: A single tab-delimited text file with gene expression measurements for genes (rows) for each sample (columns)

source_name: Liver

extract_protocol:
Tissue samples were frozen in liquid nitrogen and stored at -80 °C until RNA preparation
RiboZero RNA protocol

treatment_protocol: Parental strain animals were fed a standard breeding diet (SBD). F1-animals were fed a high fat diet (HFD) from weaning at 21 days until 70 days when offspring was euthanized and dissected

value: F1 (matBFMI)

value: Liver

value: 10 weeks


title: Sample 2: female whole-body x10


title: male Offspring 1 (matBFMI)


title: Sample 6: female whole-body x10


title: Sample 3: female whole-body x10


title: Sample 4: female whole-body x10


title: Sample 1: female whole-body x10


title: female BFMI

value: female


title: male B6N


title: male Offspring 2 (patBFMI)

value: F1 (patBFMI)


title: male Offspring 3 (patBFMI)


title: male BFMI


title: female B6N


title: D6 EB shHoxBlinc +dox

city: Gainesville

first: Lei

last: Zhou

state: FL

department: Molecular Genetics and Microbiology

institute: University of Florida

data_processing: Reads were mapped with Bowtie2 to mm9 and normalized to obtain RPKM.

source_name: day 6 embryonic bodies

growth_protocol: Murine ES cell lines, R1/E(ATCC SCRC-1036) and CGR8 MHC-GFP were maintained at a density between 4×104 and 2×105 cells/cm2 on irradiated MEFs using standard conditions. For differentiation, ES cells were seeded at a density of 4 × 105 ES cells per gelatinized 25-cm2 flask with 5 ml ES-IMDM medium without feeder cells for two days. ESCs were then dispersed into single cell suspension by trypsinization, resuspended in EB media [IMDM supplemented with 15% FBS, 180 mg/ml transferrin, 4.5×10-4 M (MTG), 50ng/ml ascorbic acid, and 1% penicillin/streptomycin], and plated on polyHEMA-coated cell culture dishes. 2ug/ml of doxycycline was added to the differentiation media at day 2 to induce knockdown.

extract_protocol:
RNA was extracted from day 6 EBs using the QIAGEN Rneasy Mini Kit.
Paired end RNA-Seq was performed by Otogenetics according to standard protocols.

value: ESC-derived embryonic bodies


title: D6 EB shHoxBlinc -dox


title: SJLCH015307_D1-MSKLCH24_D

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Samples with reads spanning multiple lanes were merged.
Gene FPKMs were computed by summing the transcript FPKMs for each gene using Cuffdiff2.
For fusion detection, reads were processed using the FusionCatcher and TopHat-Fusion software packages.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited table of log2 FPKM values.

source_name: blood cells

extract_protocol:
TRIZOL RNA Isolation Protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hematopoietic

tag: diagnosis

value: Erdheim Chester Disease


title: SJLCH015308_D1-MSKLCH25_D


title: SJLCH011812_D1-MSKLCH15T


title: SJLCH011282_D1-SJLCH14

value: Langerhans Cell Histiocytosis


title: SJLCH011811_D1-MSKLCH14T


title: SJLCH011280_D1-SJLCH09


title: SJLCH011281_D1-SJLCH13

value: Juvenile Xanthogranuloma


title: SJLCH011276_D1-SJLCH05


title: SJLCH011275_D1-SJLCH04


title: SJLCH011273_D1-SJLCH02


title: SJECD015310_D1-MSKECD20_D


title: male Offspring 1 (patBFMI)

value: male


title: MLXDN-INPUT1

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameter) to align the reads to mouse genome mm9 (MGSCv37 from Sanger).
marked duplicated reads with Picard (version 1.65(1160)) with only non-duplicated reads kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295))
To quality control (QC) the data and estimate the fragment size, the non-duplicated version of SPP (version 1.11) has been used to draw cross-correlation with support of R (version 2.14.0) using the packages caTools (version 1.17) and bitops (version 1.0-6). All our data passed QC following ENCODE criterion. MACS2 ( version 2.0.9 20111102, nomodel with extsize defined as fragment size estimated above ) have been used to call peaks.
Genome_build: mm9
Supplementary_files_format_and_content: peak call files from MACS

growth_protocol: C2C12 myoblasts were transducted by lentivirus constructs containing MLX-WT, MLX-DN sequence with empty vector (EV) and non-targetting shRNA controls.

extract_protocol:
For ChIP-sequencing, libraries were prepared from 10 ng DNA using the NEB Next ChIP-Seq Library Prep Reagent Set for Illumina with NEB Next High-Fidelity 2x PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation; the Ampure size selection step prior to PCR was eliminated; the 72C extension step of the PCR was lengthened to 45 s.
Completed libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent Technologies) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (PerkinElmer) Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies) and Kapa Library Quantificaiton kit (Kapa Biosystems) or low pass sequencing on a MiSeq nano kit (Illumina). Fifty cycle single end sequencing was performed on an Illumlina HiSeq 2500 for DNA obtained from MLX-WT and MLX-DN samples immunoprecipitated for acetylated histone H4 with three replicates for each sample including input chromatin as control.

value: myoblasts

tag: transduced with

value: MLX DN


title: MLXDN-INPUT2


title: MLXWT-INPUT2

value: MLX WT


title: MLXWT-INPUT1


title: MLXDN-INPUT3


title: MLXWT-H4AC2

description: Histone H4 Acetylation mark in MLX WT sample

tag: chip antibody

value: Rabbit Anti-acetyl-histone H4

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: MLXWT-H4AC1

tag: cell line

tag: cell type


title: MLXDN-H4AC2

description: Histone H4 Acetylation mark in MLX down sample


title: MLXDN-H4AC3


title: MLXWT-H4AC3


title: MLXDN-H4AC1


title: Adrenal medulla, group 3 [RNA-Seq]

city: Stanford

first: Mark

last: Krasnow

state: CA

address: 279 Campus Dr

institute: Stanford School of Medicine

description:
Gene expression data from adult adrenal medulla
AM #3

data_processing:
Basecalls were performed using Bustard 1.4.0
RNAseq reads were aligned to the mm9 genome assembly using Bowtie 0.9.8, allowing up to 4 mismataches in the first 32 bases for a sequence to be assigned to a specific gene ID
Python script was used to sum the counts for all isoforms of each gene (when applicable)
Counts were normalized by the length of the longest isoform of each gene (calculated using mm9)
Genome_build: mm9
Supplementary_files_format_and_content: RPKM_all.txt was generated by using Bowtie followed by Python

source_name: Mouse adrenal medulla, adult

growth_protocol: Adult

extract_protocol:
Samples were collected over two days and stored in RNAlater at 4°C. Tissue was disrupted with a grinder in Buffer RLT (Qiagen), and total RNA was purified using RNeasy Micro Kit (Qiagen).
Total RNA was amplified using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion).  aRNA was fragmented using RNA Fragmentation Reagents (Ambion).  Library was then constructed following Illumina's protocol using reagents assembled from Illumina, Invitrogen, and New England Biolabs.

treatment_protocol: No treatment

tag: tissue

value: Adrenal medulla

tag: developmental stage

value: Adult

value: C57/BL6 (Charles River, stock number 027)


title: Adrenal medulla, group 1 [RNA-Seq]

description:
Gene expression data from adult adrenal medulla
AM #1


title: SJLCH011279_D1-SJLCH08


title: SJLCH011278_D1-SJLCH07


title: Carotid body, group 2 [RNA-Seq]

description:
Gene expression data from adult carotid body
CB #2

source_name: Mouse carotid body, adult

value: Carotid body


title: THUN-12 on wheat

city: Zurich

first: Fabrizio

last: Menardo

address: Zollikerstrasse 107

country: Switzerland

institute: University of Zurich

data_processing:
Mapping: STAR,  --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04
featureCounts
edgeR, Tagwise normalization
Genome_build: Bgt_genome v1_1,  ANZE00000000
Supplementary_files_format_and_content: featureCounts

organism: Blumeria graminis

source_name: infected leaves 48h dpi

growth_protocol: 20 degrees celsius, 12h light 12 h dark

extract_protocol:
miRNeasy mini kit (Qiagen)
standard FGCZ

treatment_protocol: infection on wheat (Chinese Spring) or triticale (Timbo)

tag: host

value: wheat


title: T3-8 on triticale

value: triticale


title: 1hUV-B-3

city: Geneva 14

first: PIerre

last: Burkhard

address: 4 rue Gabrielle-Perret-Gentil

department: Department of Clinical Neurosciences

institute: HUG

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
The reads were mapped using TopHat v.2 to the Chlamydomonas reinhardtii 236 release reference (Phytozome v9.1)
The gene features were counted with HTSeq v0.5.3p9 (htseq-count). Normalization and differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.4.2
Genome_build: 236 (Phytozome v9.1)
Supplementary_files_format_and_content: tab-delimited text file with normalized counts in cpm (count per million) for each Sample and excel file with Chlamydomonas genes exhibiting differential expression following 1h narrowband UV-B exposure.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas culture cells exposed to 1h UV-B

growth_protocol: Tris acetate phosphate (TAP) media was used throughout experiment. Sufficient starting Chlamydomonas reinhardtii culture volume of 0.5x106 cells/mL was obtained by diluting a 2-day-old 10 mL starter culture grown in an Erlenmeyer flask, then six 15mL cultures were grown in deep petri dishes for four days. Plate culture were placed in a weak-light field where they were exposed to 3.6 µmol m-2 s-1 PAR (measured with a LI-250 Light Meter; LI-COR Biosciences).

extract_protocol:
2 mL of each culture was sampled following UV-B treatment and pellets of cells were frozen immediately. Total RNA was extracted with a NucleoSpin RNA II Total RNA isolation kit (Machery-Nagel). Purified RNA was treated using an RNase-Free DNase Set (Qiagen). DNase was heat inactivated in the presence of 2 mM EDTA.
The libraries were prepared with 400 ng of total RNA as starting material and processed with the Illumina Truseq mRNA stranded kit according to the manufacturer instruction. The Accuprime High Fidelity PCR enzyme was used in the DNA fragment enrichment step.

treatment_protocol: Plate cultures were placed in a light field of weak light (3.6 µmol m-2 s-1) with supplemental narrowband UV-B  (0.07 mW/cm2, measured with a VLX-3W UV Light Meter equipped with a CX-312 sensor; Vilber Lourmat) using Osram L18W/30 white-light and Philips TL20W/01RS narrowband UV-B tubes. UV-B was either applied or blocked using filters of the WG series (Schott Glaswerke) with half-maximal transmission at 311 nm and 360 nm, respectively. 2 mL of each culture was sampled following 1h treatment and pellets of cells were frozen immediately.

tag: growth stage

value: Stationary culture

value: 1h UV-B


title: 1hUV-B-2


title: MLXWT-INPUT3


title: noUV-B-3

source_name: Chlamydomonas culture cells not exposed to UV-B

value: no UV-B


title: 1hUV-B-1


title: noUV-B-2


title: noUV-B-1


title: male Offspring 2 (matBFMI)

value: F1 (matBFMI)

value: Liver

tag: age

value: 10 weeks

tag: gender


title: Adrenal medulla, group 2 [RNA-Seq]

description:
Gene expression data from adult adrenal medulla
AM #2

tag: strain


title: T3-8 on wheat


title: Mouse Islet polyA RNA-Seq in Bmal1flx/flx islets biological replicate 3

status: Public on Nov 10 2015

city: Chicago

last: Perelis

state: IL

address: 303 E Superior Street Lurie Research Center Rm 7-220

institute: Northwestern University

data_processing:
The data was analyzed by RNA Express v1.0 in BaseSpace
Reads were aligned to mm10 using STAR with the following parameters: readFilesCommand zcat outFilterType BySJout outSJfilterCountUniqueMin -1 2 2 2 outSJfilterCountTotalMin -1 2 2 2 outFilterIntronMotifs RemoveNoncanonical genomeLoad LoadAndKeep
Gene expression levels were computed by a proprietary alogorithm in BaseSpace
Differential expression was performed with DESeq2 using default parameters
Gene cycling data was computed with eJTK_Cycle
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files showing gene cycling data

source_name: Bmal1flx/flx mice

growth_protocol: Islet cells were cultured in RPMI 1640 supplemented with 1% pennicillin/streptomycin, 1% L-glutamine, and 10% FBS (mouse) or 10% human AB serum (human)

extract_protocol:
Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase
Illumina stranded LT kit for RNA-Seq

treatment_protocol:
Isolated at ZT2
For time series experiments circadian rhythms were entrained by a 1 hr forskolin pulse (10uM) and allowed to recover for 40 hrs prior to collecting the first time point

value: Pancreatic islet cells

tag: genotype


title: Mouse Islet polyA RNA-Seq in PdxCre;Bmal1flx/flx islets biological replicate 1

source_name: PdxCre;Bmal1flx/flx mice


title: Mouse Islet polyA RNA-Seq in Bmal1flx/flx islets biological replicate 1


title: Mouse Islet polyA RNA-Seq in PdxCre;Bmal1flx/flx islets biological replicate 2


title: Mouse Islet polyA RNA-Seq in PdxCre;Bmal1flx/flx islets biological replicate 3


title: Carotid body, group 1 [RNA-Seq]

description:
Gene expression data from adult carotid body
CB #1


title: PDX1

description:
Antibody: Novus Cat #NB110-40666 Lot #2430400
peak calling normalized to BetaTC6Input1.fq.gz (GSM1824092)

data_processing:
Alignment: Raw sequence reads were aligned to the mm10 reference genome and displayed using UCSC annotated genes using bowtie version 1.1.1 with parameters “--best” and “-m 1” to ensure reporting of uniquely mapped reads (tags)
Peak calling: Peaks were called using Homer “findPeaks” and specifying “-style factor” for BMAL1, CLOCK, and PDX1 and “-style histone” for H2A.Z, H3K4Me2, and H3K27A. ChIP-Seq peaks were designated as regions with 4-fold enrichment over both the input sample and the local background and were normalized to 10 million reads using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Peaks that were identified with Homer; in BED format

growth_protocol: Beta-TC6 cells were purchased from ATCC (CRL-11506) and cultured in DMEM supplemented with 15% FBS, 1% L-glutamine, and 1% penicillin/streptomycin. All cells used in experiments were at fewer than 15 passages.

extract_protocol:
Beta-TC6 cells (~40-160 million) were fixed for 30 minutes in 2mM DSG and for 10 minutes in 1% formaldehyde and then either frozen at -80ûC or processed immediately. Nuclei were isolated in buffer containing 1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.0, and protease inhibitors and sonicated using a Diagenode Bioruptor to shear chromatin to 200-1000bp fragments. Protein-DNA complexes were incubated with antibodies against BMAL1 and CLOCK (affinity-purified guinea pig IgGs as described above), H3K4Me2 (Abcam), H3K27Ac (Active Motif), H2AZ (Active Motif), or PDX1 (Novus Biologicals) and immunoprecipitated with IgG paramagnetic beads (Invitrogen). Eluted chromatin was isolated using MinElute PCR purification columns (Qiagen).
Sequencing libraries were generated using KAPA DNA Library Preparation kits (Kapa Biosystems, KK8504) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and qPCR-based quantification (Kapa Biosystems)

treatment_protocol: Cells were harvested when they reached confluence.


title: H3K4Me2

description:
Antibody: Abcam Cat #ab32356 Lot #YI061501S2
peak calling normalized to BetaTC6Input1.fq.gz (GSM1824092)


title: Input control for BMAL1 CLOCK and H2A.Z ChIP-Seq

description: Antibody: none (input)

source_name: input control


title: Mouse islet polyA RNA-Seq biological replicate 3 CT44

source_name: C57BL/6 wild type mice

treatment_protocol:
Synchronization by 1 hr forskolin pulse
For time series experiments circadian rhythms were entrained by a 1 hr forskolin pulse (10uM) and allowed to recover for 40 hrs prior to collecting the first time point

value: wild type

tag: time (hours)


title: Input control for PDX1 H3K4Me2 and H3K27Ac ChIP-Seq

description: Antibody: none (input)


title: Carotid body, group 3 [RNA-Seq]

description:
Gene expression data from adult carotid body
CB #3


title: Mouse islet polyA RNA-Seq biological replicate 3 CT36


title: H2A.Z

description:
Antibody: Active Motif Cat. #39113 Lot #01008001
peak calling normalized to BetaTC6Input1.fq.gz (GSM1824092)


title: CLOCK

description:
Antibody: Affinity-purified guinea pig serum
peak calling normalized to BetaTC6_PooledInput2.fq.gz (GSM1824093)


title: Mouse islet polyA RNA-Seq biological replicate 3 CT28


title: Mouse islet polyA RNA-Seq biological replicate 3 CT020


title: Mouse islet polyA RNA-Seq biological replicate 3 CT24


title: Sample 20: female whole-body x10

tag: foundress number

tag: host type given

value: fresh


title: Mouse islet polyA RNA-Seq biological replicate 3 CT16


title: Mouse islet polyA RNA-Seq biological replicate 3 CT40


title: THUN-12 on triticale


title: Mouse islet polyA RNA-Seq biological replicate 3 CT12


title: Mouse islet polyA RNA-Seq biological replicate 3 CT4


title: Mouse Islet polyA RNA-Seq in Bmal1flx/flx islets biological replicate 2


title: Mouse islet polyA RNA-Seq biological replicate 3 CT8


title: H3K27Ac

description:
Antibody: Active Motif Cat #39133 Lot #01613007
peak calling normalized to BetaTC6Input1.fq.gz (GSM1824092)


title: Mouse islet polyA RNA-Seq biological replicate 2 CT44


title: Mouse islet polyA RNA-Seq biological replicate 3 CT0


title: BMAL1


title: Mouse islet polyA RNA-Seq biological replicate 2 CT36


title: Mouse islet polyA RNA-Seq biological replicate 2 CT24


title: Mouse islet polyA RNA-Seq biological replicate 2 CT28


title: Mouse islet polyA RNA-Seq biological replicate 2 CT020


title: Mouse islet polyA RNA-Seq biological replicate 2 CT16


title: Mouse islet polyA RNA-Seq biological replicate 2 CT12


title: Mouse islet polyA RNA-Seq biological replicate 3 CT32


title: Mouse islet polyA RNA-Seq biological replicate 2 CT8


title: Mouse islet polyA RNA-Seq biological replicate 2 CT4


title: Mouse islet polyA RNA-Seq biological replicate 2 CT0


title: Mouse islet polyA RNA-Seq biological replicate 1 CT44


title: Mouse islet polyA RNA-Seq biological replicate 1 CT40


title: Mouse islet polyA RNA-Seq biological replicate 1 CT36


title: Mouse islet polyA RNA-Seq biological replicate 1 CT32


title: Mouse islet polyA RNA-Seq biological replicate 1 CT28


title: Mouse islet polyA RNA-Seq biological replicate 1 CT020


title: Mouse islet polyA RNA-Seq biological replicate 1 CT12


title: Mouse islet polyA RNA-Seq biological replicate 1 CT8


title: Mouse islet polyA RNA-Seq biological replicate 1 CT24


title: Mouse islet polyA RNA-Seq biological replicate 2 CT32


title: Mouse islet polyA RNA-Seq biological replicate 1 CT16


title: Mouse islet polyA RNA-Seq biological replicate 1 CT0


title: Mouse islet polyA RNA-Seq biological replicate 2 CT40


title: XTO-Xiwi_CLIPseq_repB

city: BOSTON

first: NELSON

middle: C

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

description: Piwi associated RNA fragments

data_processing:
fastx_clipper from fastx_toolkit-0.0.13.2 to remove the 3' adapter sequence with paramaters "-M 9 -n -l 20"
5' and 3' adapter sequences were removed Xiwi and Xili sRNAseq reads using a custom perl script.
Genome_build: n/a
Supplementary_files_format_and_content: counts

organism: Xenopus tropicalis

source_name: ovary

extract_protocol:
Whole cell lysates for CLIP were generated by lysing in Q-column buffer (20mM Hepes-KOH pH 7.9; 10% glycerol; 0.1 M KOAc; 0.2 mM EDTA; 1.5 mM MgCl2; 0.5 mM DTT; 1X Roche Complete EDTA-free Protease Inhibitor Cocktail; 0.5% NP40), dounced with 50 strokes and sonicated 2 rounds for 30 secs.  mRNA was CLIP RNA fragments were extracted with Trizol. mRNAs were further isolated by the Magnetrac Atail selection kit. The two antibodies used are not sold from a manufacturer but were custom made.  The mouse monoclonal antibody against Piwi was obtained from the Siomi lab (Saito et al. Genes Dev. 2006 Aug 15;20(16):2214-22.) while the rabbit polyclonal antibody against Piwi was generated by the Lau lab with a peptide antigen to the N terminal 12 amino acids of the Piwi gene. For  RIPseq, sRNAseq and oocyte RNAseq experiments, whole cell lysates were generated from stage 1-3 oocytes only. Both ovaries were dissected from an adult frog and the oocytes were liberated from the follicle cells by cutting the ovaries into ~3mm2 peices and incubating them in 3mg/mL collagenase in 0.1M Sodium Phosphate pH 7.4 for ~1hour. Liberated oocytes were then washed into Modified Barth's Saline (5mM HEPES-KOH pH 7.8, 88mM NaCl, 1mM KCl, 1mM MgSO4, 2.5mM NaHCO3, 0.7mM CaCl2) and passed through a 450µm mesh screen to separate out the stage 1-3 oocytes. Stage 1-3 oocytes were washed into XB buffer (10mM HEPES-NaOH pH7.7, 1mM MgCl2, 0.1mM CaCl2, 100mM KCl, 50mM Sucrose, 1x Protease inhibitor mix) and Dounced with 2 strokes. Lysed oocytes were spun at 20,000xg for 5 minutes at 4˚C. The middle layer containing cytosol and organelles was saved as the stage 1-3 oocyte extract.
CLIP tags and one set of mRNA sequencing libraries were generated with custom protocol for constructing small RNA libraries (Robine et al, Curr Bio 2009).  All other mRNA libraries were constructed with the ScriptSeq version 1 and version 2 kits from Epicenter Biotech. RIPseq and XL_Oocyte_RNAseq libraries were generated using the Illumina Tru-Seq RNA kit. Xiwi and Xili sRNAseq libraries were constructed using a linker ligation protocol adapted from a custom protocol (Ingolia et al, Nature Protocols 2012).

treatment_protocol: For CLIP, cells were irradiated with 254nm UV light with 0.9j/cm2 of energy.  For mRNA-Seq experiments, the oocytes were not treated prior to extract preparation.

value: oocyte

tag: Sex

value: female


title: XTO_Stg56_RNAseq

description: Poly-A RNA


title: XTO-Xiwi_CLIPseq_repA

description: Piwi associated RNA fragments


title: XTO-Xili-CLIPseq

description: Piwi associated RNA fragments


title: XTO_Stg34_RNAseq

description: Poly-A RNA


title: Human islet polyA RNA-Seq donor 3 CT16

source_name: Human donor IIDP ID 1174


title: Human islet polyA RNA-Seq donor 3 CT12


title: Laublab_NA1000_ML2297_Pxyl-gcrA-3xFLAG_PYEX_Rifampicin_AntiFlag_ChIPSeq

city: Berkeley

first: Diane

last: Haakonsen

address: 330 Li Ka Shing

department: MCB

institute: Berkeley

data_processing:
Reads were mapped to the Caulobacter crescentus NA1000 reference genome using BWA
Read extension and pile-up from uniquely mapping reads was performed using the MACS software package 1.4.2 (Zhang et al. 2008) (with d=200 and keeping all tags at the same location) yielding 10 bp genomic bins.
The data were further process using custom scripts written in Python 2.7.3. The data were smoothed by convolution with a Gaussian (μ=0, σ=50bp, x=(-200 bp, +200 bp)). The data were then normalized in reads per million (rpm).
Genome_build: NC_011916.1
Supplementary_files_format_and_content: wig files conform to the UCSC format and can be viewed using the genome browser from the Broad Institute IGV 2.3.57.

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus CB15N

growth_protocol:
Cells were grown in PYE +0.3% xylose, and incubated with 25ug/ml Rifampicin for 30 min before fixation with 1% formaldehyde
Caulobacter crescentus were grown in PYE at 30C  as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid) [ug/ml]): kanamycin (5), oxytetracycline (1). Cells were fixed with 1% formaldehyde.  For rifampicin treatment, cells were incubated with  25 ug/ml rifampicin (final concentration) for 30 minutes before fixing with formadehyde.

extract_protocol:
Cells were lysed and DNA sheared by sonication and protein-DNA complexes were isolated with indicated antibody
Libraries were generated on a Beckman-Colter Genomics SPRIworks system using 200-400 bp size selection and amplified 12-16 cycles

tag: strain background

tag: genotype/variation

tag: treated with

value: 25 ug/ml rifampicin (final conc.) for 30 min

tag: chip antibody

value: anti-FLAG

tag: chip antibody vendor

value: Sigma-Aldrich


title: Laublab_NA1000_ML2299_rpoC-3xFLAG_PYE_AntiFlag_ChIPSeq

growth_protocol:
Cells were grown in PYE and fixed with 1% formaldehyde
Caulobacter crescentus were grown in PYE at 30C  as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid) [ug/ml]): kanamycin (5), oxytetracycline (1). Cells were fixed with 1% formaldehyde.  For rifampicin treatment, cells were incubated with  25 ug/ml rifampicin (final concentration) for 30 minutes before fixing with formadehyde.

tag: chip antibody cat. #


title: Human islet polyA RNA-Seq donor 3 CT8

tag: cell type


title: Laublab_NA1000_ML2297_Pxyl-gcrA-3xFLAG_PYEX_AntiFlag_ChIPSeq

growth_protocol:
Cells were grown in PYE +0.3% xylose and fixed with 1% formaldehyde
Caulobacter crescentus were grown in PYE at 30C  as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid) [ug/ml]): kanamycin (5), oxytetracycline (1). Cells were fixed with 1% formaldehyde.  For rifampicin treatment, cells were incubated with  25 ug/ml rifampicin (final concentration) for 30 minutes before fixing with formadehyde.


title: H3 Q120M, K121P, K125Q replicate 2

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: UBC

description: DNA purified from Mnase-digested chromatin

data_processing:
Reads were aligned to the saccer3 genome using BWA
Samtools was used to filter for mapped reads with a mapping quality score of at least 10
Reads smaller than 500bp were selected for using AWK
Read coverage wig files were generated using the java-genomics-toolkit base.align.count function
Genome_build: saccer3
Supplementary_files_format_and_content: Wig file: coverage at one base pair resolution

source_name: yeast

growth_protocol: One hundred milliliters of S. cerevisiae cultures were grown to an A600 of 0.8.

extract_protocol:
Thawed cell pellets were resuspended in 600 μL of 50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, Roche protease inhibitor cocktail (PIC) and 0.2 mM PMSF and lysed by bead beating. The resulting lysate was centrifuged at 15,000g for 30 minutes and the chromatin pellet was washed and resuspended in 900 μL NP-S buffer (0.5 mM sperimidine, 1 mM β-ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris-Cl pH = 7.4, 5 mM MgCl2, 1 mM CaCl2, EDTA-free PIC, 2mM PMSF). The resuspended pellet was added to 100μL NP-S buffer containing 200 units micrococcal nuclease (MNase) and incubated at 37°C for 1 hour. The reaction was stopped by addition of EDTA to 10 mM. Crosslinks were reversed by the addition of 1% SDS and 40 μg proteinase K followed by incubation at 65 °C overnight. DNA was purified by PCI extraction and RNase A treated.
Library construction for the Illumina platform was performed using a custom procedure for paired-end sequencing. Briefly, 2–10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. In between each reaction, the material was purified using phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation. The resulting material was then amplified in the Phusion HF master mix (NEB) using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5′ AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3′, where “NNNNNN” corresponds to unique hexamer barcodes]. PCR amplification was performed as follows: denaturation at 98 °C for 60 s; eight cycles of (98 °C, 30 s; 65 °C, 30 s; 72 °C, 30 s), and a final extension at 72 °C for 5 min. Amplified libraries were purified using 0.8 (vol) Agencourt AMPure XP solid phase reversible immobilization paramagnetic beads and eluted in 10 mM Tris⋅HCl pH 8.5. An aliquot of each library was run on an Agilent High Sensitivity chip to check the size distribution and molarity of the PCR products.    Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200–600 bp size range were selected on an 8% (wt/vol) Novex TBE PAGE gel (Invitrogen). An aliquot (1 μL) of the library pool was run on an Agilent High Sensitivity chip to confirm proper size selection and measure DNA concentration. The pooled libraries were diluted to 15 nM and their concentration was confirmed using the Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen).

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 15 minutes before quenching the reaction with 125 mM glycine. Cells were washed three times with 1 mL 10 mM Tris-Cl pH = 7.5, 100 mM NaCl and frozen at -80°C.

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 (hht1-hhf1)::LEU2 (hht2-hhf2)::KAN pHHF2-hht2.Q120M,K121P,K125Q

value: H3 c-terminal mutant


title: XTT-Xiwi_CLIPseq

description: Piwi associated RNA fragments

source_name: testes

value: spermatocytes and spermatids

value: male


title: Human islet polyA RNA-Seq donor 3 CT4


title: Human islet polyA RNA-Seq donor 3 CT20


title: Laublab_NA1000_ML2296_Pxyl-gcrA_PYEX_AntiFlag_Control_ChIPSeq

value: {delta}gcrA(tetR); Pxyl-gcrA(kanR)


title: XL_Oocyte_RNAseq

description: Poly-A RNA

organism: Xenopus laevis

value: Stage 1-3 oocytes


title: Human islet polyA RNA-Seq donor 3 CT0


title: Mouse islet polyA RNA-Seq biological replicate 1 CT4


title: H3 Q120M, K121P, K125Q replicate 1


title: wt replicate 2

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 (hht1-hhf1)::LEU2 (hht2-hhf2)::KAN pHHF2-HHT2

value: wildtype


title: Human islet polyA RNA-Seq donor 2 CT20

source_name: Human donor IIDP ID 1121


title: XL_Xili_IP_sRNA

description: Piwi associated small RNAs


title: XL_Xili_RIPseq

description: Piwi associated RNA fragments


title: XL_Xiwi_RIPseq

description: Piwi associated RNA fragments


title: wt replicate 1


title: Human islet polyA RNA-Seq donor 2 CT16


title: XL_Xiwi_IP_sRNA

description: Piwi associated small RNAs


title: Human islet polyA RNA-Seq donor 2 CT8


title: Human islet polyA RNA-Seq donor 1 CT20

source_name: Human donor IIDP ID 1114


title: Laublab_NA1000_WT_PYE_Rifampicin_AntiRpoD_ChIPSeq

growth_protocol:
Cells were grown in PYE, and incubated with 25ug/ml Rifampicin for 30 min before fixation with 1% formaldehyde
Caulobacter crescentus were grown in PYE at 30C  as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid) [ug/ml]): kanamycin (5), oxytetracycline (1). Cells were fixed with 1% formaldehyde.  For rifampicin treatment, cells were incubated with  25 ug/ml rifampicin (final concentration) for 30 minutes before fixing with formadehyde.

value: wild-type

value: anti-RpoD

value: Neoclone


title: Human islet polyA RNA-Seq donor 2 CT0

value: Pancreatic islet cells


title: Human islet polyA RNA-Seq donor 1 CT16


title: Laublab_NA1000_ML2301_sigma54-3xFLAG_PYE_Rifampicin_AntiFlag_ChIPSeq


title: Human islet polyA RNA-Seq donor 1 CT8


title: Human islet polyA RNA-Seq donor 1 CT12


title: SET4 L1 spikein rep2 RNAseq

status: Public on Nov 09 2015

first: Sevinc

last: Ercan

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description:
mRNA
RNAseq_spikeins_counts.txt
RNAseq_spikeins_counts_Cbriggsae.txt

data_processing:
Basecalls were performed using CASAVA version 1.8.
RNA-seq reads were aligned to the WS220 genome assembly using tophat version 2.0.11 using default parameters for a stranded library.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.2.0 using default parameters supplying gene annotations.
Raw counts for each gene were generated using htseq-count version 0.6.0 using default parameters.
Genome_build: WS220
Supplementary_files_format_and_content: FPKM text file contains the FPKM values for each gene for each replicate.

organism:
Caenorhabditis briggsae
Caenorhabditis elegans

source_name: whole worms

growth_protocol: Larvae were collected after overnight embryo hatching and growth for 6 hours (L1) or 24 hours (L3) on NGM plates.

extract_protocol:
RNA was extracted by freeze cracking samples by freezing in liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA RNA was cleaned up through Qiagen RNeasy column.
mRNA was purified from .5-10 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212

treatment_protocol: Packed larvae were resuspended in 10V of Trizol and frozen at -80C.

tag: developmental stage


title: SET4 L1 spikein rep3 RNAseq


title: Human islet polyA RNA-Seq donor 1 CT4


title: Human islet polyA RNA-Seq donor 1 CT0


title: Laublab_NA1000_ML2299_rpoC-3xFLAG_PYE_Rifampicin_AntiFlag_ChIPSeq


title: N2 L1 spikein rep3 RNAseq


title: N2 L1 spikein rep2 RNAseq


title: P7_Id4

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to mm9 whole genome using tophat version 2.0.9 with parameters : -p 8 --splice-mismatches 1  --segment-mismatches 2 --solexa1.3-quals
FPKM and differential expression were calculated using the Cufflinks suite version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Testis

extract_protocol:
Cells were isolated from C57Bl/6 mice at postnatal day 0,7,12,14 (labeled P0 to P14 respectively). These cells were further selected for specific markers (Oct4, Thy1, Id4 or Kit).
Cell populations labeled with GFP were selected for GFP via FACS. FACS analysis involved isolations from P0 Vasa-GFP+ (JAX Lab, 006954), P0 and P7 Oct4-GFP+ (JAX Lab, 008214); and P7Id4-GFP+ (J. Oatley). Cells were sorted using FACSCalibur (BD Biosciences, SanJose, CA). The percentage of live cells was >95%, by exclusion of propidium iodide.
Isolation of either the THY1+ or c-KIT+ stem cell subtypes from C57Bl/6 mice was carried out with a magnetic cell-sorting (MACS) separator (MiltenyiBiotec, Bergisch-Gladbach, Germany) using anti-CD117 (KIT) antibody or anti-CD90.2 (THY1) (MiltenyiBiotec).
Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit (Cat # 80004), ribosomal RNA was depleted using RiboZero kit.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

tag: cell markers

value: Spermatogonia

value: postnatal day 7


title: P0_Oct4GFP

tag: age

value: postnatal day 0


title: Human islet polyA RNA-Seq donor 2 CT12


title: P7_VasaThy1


title: Human islet polyA RNA-Seq donor 2 CT4


title: Laublab_NA1000_WT_PYE_AntiRpoD_ChIPSeq


title: wdr82sh_sh790_4sU_stranded_LPS_45min

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: wdr82sh_sh790_4sU_stranded_genes.fpkm_tracking.gz

data_processing:
Library strategy: 4sU-seq
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches. For stranded samples processing the --library-type was set to fr-secondstrand or to fr-firststrand according to library preparation
Transcripts abundance were quantified using Cufflinks 2.1.1 (PMID: 20436464)
Differentially expressed genes were called using Cuffdiff 2.1.1 (PMID: 23222703)
Analysis of RNA synthesis and degradation ratess was carried out using INSPEcT (PMID: 25957348). Raw counts are provideded as processed files.
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63 or https://bioconductor.org/packages/release/data/annotation/html/TxDb.Mmusculus.UCSC.mm9.knownGene.html
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM) (refer to http://cufflinks.cbcb.umd.edu/manual.html for details); *.exons_gr1.counts.txt list the raw counts calculated using UCSC_mm9_genes_sicer.gtf; *.introns_gr2.counts.txt list the raw counts calculated using UCSC_mm9_introns_sicer.gtf; *.exons_gr1.counts.txt and *.introns_gr2.counts.txt have two columns: 1) the IDs from either UCSC_mm9_genes_sicer.gtf or UCSC_mm9_introns_sicer.gtf;; 2) the raw count calculated for the indicated sample.   UCSC_mm9_genes_sicer.gtf and UCSC_mm9_introns_sicer.gtf have been generated using the makeGtfFromDb function from the compEpiTools package (R/Bioconductor, http://www.bioconductor.org/packages/release/bioc/html/compEpiTools.html). The GTFs are based on both the known gene annotations from UCSC (https://bioconductor.org/packages/release/data/annotation/html/TxDb.Mmusculus.UCSC.mm9.knownGene.html) and extragenic blocks of aberrant transcriptions as defined in Supp. Table S4. Counts were computed using makeRPKMs function in the INSPEcT package (R/Bioconductor, http://bioconductor.org/packages/devel/bioc/html/INSPEcT.html). The exons (defined on the Entrez ID of the corresponding genes) and the extragenic blocks (identified using the following nomenclature: extRNA_[closest gene]_[TES/TSS]) were appended to the UCSC_mm9_genes_sicer.gtf. The intronic coordinates (defined on the Entrez ID of the corresponding genes) were instead appended to the UCSC_mm9_introns_sicer.gtf. Both GTFs are defined on the following columns: 1) chromosome (mm9); 2) source (either UCSC known genes or extragenic regions of transcription); 3) feature (always defined as exon); 4) start coordinate (mm9); 5) end coordinate (mm9); 6) score (empty); 7) strand; 8) frame (empty); 9) attribute (see previous paragraph for details).

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: At day zero bone marrow cells were isolated from FVB/hsd mice and 3 × 10^6 cells/well in a 6-well plate were seeded in BM medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cells were infected two times pr day for two days consecutive days after plating, using supernatants from transfected Phoenix-ECO packaging cells. After the last infection, cells where transferred to 10 cm culture plates, and puromycin selection (3.5 μg/ml) was started.

extract_protocol:
For sequencing of ribosomal-RNA depleted total RNA, RNA was isolated with RNeasy (Qiagen) with DNAse I treatment. Then, the Illumina kit TruSeq stranded total RNA library preparation kit (RS-122-2201) was used for library synthesis. Briefly, after depletion of ribosomal RNA (Ribo-Zero), the RNA molecules are fragmented, followed by reverse transcription into cDNA with random primers in the presence of actinomycin D. Then, second strand cDNA synthesis is performed with DNA Polymerase I with dUTP instead of dTTP. Hence, the second strand will not be copied and amplified in the PCR-amplification step as the polymerase cannot go past this nucleotide. Then a single A-base is added to the 5' ends and adapters are ligated. The cDNA is a amplified with PCR (15 cycles) to generate the final cDNA library. In order to obtain nascent 4-thio-Uridine (4sU) labelled RNA, 4sU was added to the cell culture medium at a final concentration of 300 mM for 45 min before harvesting the cells. The 4sU-labeled RNA was isolated as described (Rabani M. et al., 2011). Briefly, RNA was isolated with Trizol (Invitrogen), then 50 ug of total RNA was labeled with biotin (EZ-link HPDP-biotin, Thermo Scientific), and unbound biotin was removed with MaXtract high density tubes (Qiagen). Biotinylated RNA was isolated with MyOne Streptavidin T1 Dyneabeads (Invitrogen) for 15 min at room temperature, followed by washing of the beads according to manufacturers instructions. The 4sU-labelled RNA was finally eluted with 95% Formamide (Sigma) in 10 mM EDTA at 65¡C for 10 min, and purified on RNeasy MinElute spin columns (Qiagen), and eluted in 14 ul H2O. A total of 40-100 ng of 4sU-labelled RNA was used for cDNA-library synthesis using Illumina kits, skipping the step of either ribosomal depletion or polyA-selection, starting from the RNA fragmentation step.
TruSeq RNA Sample Preparation kit (RS-122-2001) or the kit processing the RNA to retain strand information (Truseq Stranded Total RNA Sample Preparation kit (RS-122-2201), or in the Epicentre ScriptSeq RNA-Seq Library Preparation Kit (SSV21124) was used (for second and first strand synthesis respectively). The Illumina stranded RNAseq kit are based on the dUTP method as described in Levin et. al, Nat. Methods, 2010.

treatment_protocol: BMDMs were either untreated or treated for 45 minutes with lipopolysaccharide (LPS, 10 ng/ml).

value: FVB/Hsd

value: BMDM cells (7th day of differentiation)

tag: library type

value: Stranded (first-strand synthesis)

tag: treatment

value: LPS (10 ng/ml)

tag: short hairpin


title: wdr82sh_sh830_total_stranded_UT

description:
wdr82sh_sh830_total_stranded_UT.exons_gr1.counts.txt.gz
wdr82sh_sh830_total_stranded_UT.introns_gr2.counts.txt.gz
UCSC_mm9_genes_introns.gtf.gz
UCSC_mm9_genes_sicer.gtf.gz

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches. For stranded samples processing the --library-type was set to fr-secondstrand or to fr-firststrand according to library preparation
Transcripts abundance were quantified using Cufflinks 2.1.1 (PMID: 20436464)
Differentially expressed genes were called using Cuffdiff 2.1.1 (PMID: 23222703)
Analysis of RNA synthesis and degradation ratess was carried out using INSPEcT (PMID: 25957348). Raw counts are provideded as processed files.
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63 or https://bioconductor.org/packages/release/data/annotation/html/TxDb.Mmusculus.UCSC.mm9.knownGene.html
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM) (refer to http://cufflinks.cbcb.umd.edu/manual.html for details); *.exons_gr1.counts.txt list the raw counts calculated using UCSC_mm9_genes_sicer.gtf; *.introns_gr2.counts.txt list the raw counts calculated using UCSC_mm9_introns_sicer.gtf; *.exons_gr1.counts.txt and *.introns_gr2.counts.txt have two columns: 1) the IDs from either UCSC_mm9_genes_sicer.gtf or UCSC_mm9_introns_sicer.gtf;; 2) the raw count calculated for the indicated sample.   UCSC_mm9_genes_sicer.gtf and UCSC_mm9_introns_sicer.gtf have been generated using the makeGtfFromDb function from the compEpiTools package (R/Bioconductor, http://www.bioconductor.org/packages/release/bioc/html/compEpiTools.html). The GTFs are based on both the known gene annotations from UCSC (https://bioconductor.org/packages/release/data/annotation/html/TxDb.Mmusculus.UCSC.mm9.knownGene.html) and extragenic blocks of aberrant transcriptions as defined in Supp. Table S4. Counts were computed using makeRPKMs function in the INSPEcT package (R/Bioconductor, http://bioconductor.org/packages/devel/bioc/html/INSPEcT.html). The exons (defined on the Entrez ID of the corresponding genes) and the extragenic blocks (identified using the following nomenclature: extRNA_[closest gene]_[TES/TSS]) were appended to the UCSC_mm9_genes_sicer.gtf. The intronic coordinates (defined on the Entrez ID of the corresponding genes) were instead appended to the UCSC_mm9_introns_sicer.gtf. Both GTFs are defined on the following columns: 1) chromosome (mm9); 2) source (either UCSC known genes or extragenic regions of transcription); 3) feature (always defined as exon); 4) start coordinate (mm9); 5) end coordinate (mm9); 6) score (empty); 7) strand; 8) frame (empty); 9) attribute (see previous paragraph for details).

tag: strain

value: No treatment


title: wdr82sh_sh1137_total_stranded_UT

description:
wdr82sh_sh1137_total_stranded_UT.exons_gr1.counts.txt.gz
wdr82sh_sh1137_total_stranded_UT.introns_gr2.counts.txt.gz
UCSC_mm9_genes_introns.gtf.gz
UCSC_mm9_genes_sicer.gtf.gz


title: wdr82sh_sh790_4sU_stranded_UT


title: wdr82sh_sh1137_4sU_stranded_LPS_45min

description: wdr82sh_sh1137_4sU_stranded_genes.fpkm_tracking.gz


title: wdr82sh_sh1137_4sU_stranded__UT


title: Laublab_NA1000_ML2300_sigma32-3xFLAG_PYE_Rifampicin_AntiFlag_ChIPSeq

value: 25 ug/ml rifampicin (final conc.) for 30 min

value: anti-FLAG

value: Sigma-Aldrich


description:
wdr82sh_scrambled_total_stranded_UT_rep2.exons_gr1.counts.txt.gz
wdr82sh_scrambled_total_stranded_UT_rep2.introns_gr2.counts.txt.gz
UCSC_mm9_genes_introns.gtf.gz
UCSC_mm9_genes_sicer.gtf.gz


title: P7_Oct4


title: shMenin_4sU_stranded_UT

description: shMenin_4sU_stranded_genes.fpkm_tracking.gz

value: shMenin


title: wdr82sh_scrambled_4sU_stranded_UT_rep2

description:
wdr82sh_sh1137_4sU_stranded_genes.fpkm_tracking.gz
wdr82sh_sh790_4sU_stranded_genes.fpkm_tracking.gz


title: SET4 L1 spikein rep1 RNAseq


title: wdr82sh_scrambled_4sU_stranded_LPS_45min_rep2


title: BMDMs_UT_wdr82sh_sh1137_intergenic_sx_Mpeg1

data_processing:
library strategy: 4C-seq
Reads were quality filtered according to the Illumina pipeline
Reads for different viewpoints were demultiplexed using fastq-multx (part of http://code.google.com/p/ea-utils)
4Cseqpipe (van de Werken et al. 2012) was used to map the reads and compute local coverage around viewpoints
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *.nearcis.cover.txt (refer to the 4Cseqpipe manual for full details about the format http://compgenomics.weizmann.ac.il/tanay/?page_id=367). 4Cseqpipe cis-profile around viewpoint.

growth_protocol: Bone marrow cells were isolated from C57B6/Jhsd mice and plated in 10 cm dishes for 6 days in 10 ml of BM-medium (Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 20% low-endotoxin fetal bovine serum (FBS), 30% L929 conditioned medium, 1% glutamine, 1% penicillin-streptomicin, 0.5% sodium pyruvate and 0.1% β-mercaptoethanol.). Cells were cultured for 6 days before harvesting.

extract_protocol:
4C templates were prepared as previously described (Splinter et al., 2012).  Briefly, chromatin was cross-linked with 2% formaldehyde for 10 min at room temperature, nuclei were isolated and cross-linked DNA was digested with the 4bp cutter DpnII. After proximal fragments ligation, cross-links were reverted. The second digestion was performed with the 4bp cutter Csp61 and followed again by intramolecularligation. 200 ng of the obtained 4C template were used to perform 8 individual PCR reactions, which were then pooled together and purified for HT sequencing.
Adaptor sequences necessary for Illumina single-read sequencing (Hi-seq 2000) were added to 4C primer pairs as additional 5′ overhangs

tag: viewpoint

value: 5' of the Mpeg1 gene


title: wdr82sh_scrambled_4sU_stranded_LPS_45min_rep1


title: N2 L1 spikein rep1 RNAseq


title: BMDMs_UT_wdr82sh_scrambled_intergenic_dx_Mpeg1

value: 3' of the Mpeg1 gene


title: BMDMs_UT_wdr82sh_scrambled_intergenic_sx_Mpeg1


title: wdr82sh_scrambled_4sU_stranded_UT_rep1


title: BMDMs_UT_wdr82sh_sh1137_intergenic_dx_Mpeg1


title: BMDMs_UT_wdr82sh_sh1137_intergenic_dx_Lgals3

value: 3' of the Lgals3 gene


title: BMDMs_UT_wdr82sh_scrambled_intergenic_dx_Lgals3


title: BMDMs_UT_wdr82sh_scrambled_intergenic_sx_Lgals3

value: 5' of the Lgals3 gene


title: EpiSC H3K9me2 nChIPseq4

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

institute: University of Cambridge

data_processing:
ChIP-seq reads were extended to 250nt for lcChIP and 150nt or 300nt for H3K27me3 and H3K9me2 nChIP respectively. Reads were aligned to the mouse reference genome (GRCm38/mm10) using bowtie with parameters –m 2 –v 0 (Langmead et al., 2009). Genome-wide ChIP vs. Input profiles were normalized by the total number of mapped reads per 200 nt (RPKM). In analogy, ChIP-seq vs. Input counts on promoters or gene bodies were normalized by the total number of mapped reads and by size (RPKM).
RNA-seq reads were all trimmed to 40nt and then adapter- and quality-trimmed, and aligned with Tophat2 (Kim et al., 2013) against the mouse reference (GRCm38/mm10) genome. Read counts per ENSEMBL were obtained by htseq-count (Anders et al., 2014).
Genome_build: GRCm38/mm10

source_name: EpiSC

growth_protocol: see extra colum

extract_protocol:
EpiSCs were grown in feeder-free conditions in fibronectin (Millipore) coated dishes. Culture media contained: N2B27 medium supplemented with bFGF (12 ng/ml) and ActivinA (20 ng/ml).
20 ng of immunoprecipitated or input DNA was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared library DNA was resolved on a 2% agarose gel and the dinucleosome fractions were isolated

treatment_protocol: no treatment

tag: background

value: mixed background

tag: genotype

value: X-GFP

tag: tissue/cell type

value: epiblast stem cells

tag: antibody

value: H3K9me2 (Abcam, ab1220)


title: shMenin_4sU_stranded_LPS_45min

value: FVB/Hsd


title: Epiblast Input lcChIPseq3

source_name: Epiblast E6.25

extract_protocol:
Epiblast cells were isolated from E6.25 pre-gastrulating embryos coming from outbred MF1 females crossed with ΔPE-Oct4-EGFP (GGOF) stud males. After recovering embryos from the decidua, Reichert’s membrane was dissected out and extraembryonic cone was also removed. Remaining tissue was used to prepare single cell suspension and sorting using MoFlo high-speed cell sorter (Beckman Coulter) based on EGFP expression.
lcChIP-seq was performed by using a modified published method (Ng et al., 2013). Isolated DNA was primed using WGA4 kit (Sigma). The next step involved library amplification using HiFi Library Amplification master mix (Kappa biosciences) and BpmI-primer (CCGGCCCTGGAGTGTTGGGTGTGTTTGG). These reactions were incubated in a thermocycler using following conditions: 98 °C for 3 min; 11-12 X (98 °C for 10 sec; 65 °C for 30 sec; 72 °C for 1 min); 72 °C for 7 min: or 4 °C as suggested. The number of cycles depended on the amount of DNA precipitated and so 11 cycles were used for H3K9me2 and 12 for H3K27me3. Amplified DNA was purified with Agencourt RNA clean XP beads. Adapter trimming was performed by BpmI digestion, secondary adaptor ligation and a second round of digestion (Ng et al., 2013). Digested DNA was purified with Agencourt RNA clean XP bead and used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen).

value: E6.25 dpc

value: epiblast


title: EpiLC H3K9me2 nChIPseq3

source_name: EpiLC

extract_protocol:
EpiLCs were induced for 48h from 2i/LIF ESCs as previously described (Hayashi et al., 2011).
20 ng of immunoprecipitated or input DNA was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared library DNA was resolved on a 2% agarose gel and the dinucleosome fractions were isolated

value: 2 days post induction

value: epiblast-like cells


title: Epiblast H3K9me2 lcChIPseq3


title: Epiblast H3K27me3 lcChIPseq1 2

value: H3K27me3 (Millipore, 07-449)


title: EpiSC H3K9me2 nChIPseq3


title: Epiblast H3K27me3 lcChIPseq1 1


title: Epiblast Input lcChIPseq1


title: EpiLC H3K27me3 nChIPseq2

extract_protocol:
EpiLCs were induced for 48h from 2i/LIF ESCs as previously described (Hayashi et al., 2011).
20 ng of immunoprecipitated or input DNA was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared library DNA was resolved on a 2% agarose gel and the mononucleosome fractions were isolated


title: EpiSC Input nChIPseq3


title: Laublab_NA1000_ML2298_Pgcra-gcrA-3xFLAG_PYE_AntiFlag_ChIPSeq

tag: strain background

tag: genotype/variation

value: anti-FLAG


title: EpiSC Input nChIPseq4


title: EpiSC Input nChIPseq2

extract_protocol:
EpiSCs were grown in feeder-free conditions in fibronectin (Millipore) coated dishes. Culture media contained: N2B27 medium supplemented with bFGF (12 ng/ml) and ActivinA (20 ng/ml).
20 ng of immunoprecipitated or input DNA was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared library DNA was resolved on a 2% agarose gel and the mononucleosome fractions were isolated


title: EpiSC H3K27me3 nChIPseq2


title: EpiLC Input nChIPseq1


title: EpiSC Input nChIPseq1


title: EpiSC H3K27me3 nChIPseq1


title: EpiLC H3K27me3 nChIPseq1


title: EpiLC Input nChIPseq3


title: wdr82sh_sh1137_polyA_unstranded_UT

description: supplementary file: wdr82sh_polyA_unstranded_genes.fpkm_tracking.txt

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches. For stranded samples processing the --library-type was set to fr-secondstrand or to fr-firststrand according to library preparation
Transcripts abundance were quantified using Cufflinks 2.1.1 (PMID: 20436464)
Differentially expressed genes were called using Cuffdiff 2.1.1 (PMID: 23222703)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM) (refer to http://cufflinks.cbcb.umd.edu/manual.html for details)

extract_protocol:
For sequencing of poly-A RNA, RNA was isolated with RNeasy (Qiagen) with DNAse I treatment. The Illumina kit TruSeq RNA preparation kit (RS-122-2001) with oligo-dT-based polyA-selection was used for cDNA-library synthesis. Briefly, after polyA-isolation, the RNA molecules are fragmented, followed by reverse transcription into cDNA with random primers. Then, second strand cDNA synthesis is performed with DNA Polymerase I in the presence of RNase H. The cDNA fragments are then end-repaired, a single A-base is added to the 5«ends and adapters are ligated. The cDNA is a amplified with PCR (15 cycles) to generate the final cDNA library. In order to obtain nascent 4-thio-Uridine (4sU) labelled RNA, 4sU was added to the cell culture medium at a final concentration of 300 mM for 45 min before harvesting the cells. The 4sU-labeled RNA was isolated as described (Rabani M. et al., 2011). Briefly, RNA was isolated with Trizol (Invitrogen), then 50 ug of total RNA was labeled with biotin (EZ-link HPDP-biotin, Thermo Scientific), and unbound biotin was removed with MaXtract high density tubes (Qiagen). Biotinylated RNA was isolated with MyOne Streptavidin T1 Dyneabeads (Invitrogen) for 15 min at room temperature, followed by washing of the beads according to manufacturers instructions. The 4sU-labelled RNA was finally eluted with 95% Formamide (Sigma) in 10 mM EDTA at 65¡C for 10 min, and purified on RNeasy MinElute spin columns (Qiagen), and eluted in 14 ul H2O. A total of 40-100 ng of 4sU-labelled RNA was used for cDNA-library synthesis using Illumina kits, skipping the step of either ribosomal depletion or polyA-selection, starting from the RNA fragmentation step.
TruSeq RNA Sample Preparation kit (RS-122-2001) or the kit processing the RNA to retain strand information (Truseq Stranded Total RNA Sample Preparation kit (RS-122-2201), or in the Epicentre ScriptSeq RNA-Seq Library Preparation Kit (SSV21124) was used (for second and first strand synthesis respectively). The Illumina stranded RNAseq kit are based on the dUTP method as described in Levin et. al, Nat. Methods, 2010.

treatment_protocol: BMDMs were either untreated or treated for 4 hrs with lipopolysaccharide (LPS, 10 ng/ml).

value: BMDM cells (7th day of differentiation)

value: Unstranded

value: No treatment


title: wdr82sh_sh1137_4sU_stranded_UT

description: supplementary file: wdr82sh_4sU_stranded_genes.fpkm_tracking.txt

data_processing:
Library strategy: 4sU-seq
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches. For stranded samples processing the --library-type was set to fr-secondstrand or to fr-firststrand according to library preparation
Transcripts abundance were quantified using Cufflinks 2.1.1 (PMID: 20436464)
Differentially expressed genes were called using Cuffdiff 2.1.1 (PMID: 23222703)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM) (refer to http://cufflinks.cbcb.umd.edu/manual.html for details)

value: Stranded (second-strand synthesis)


title: wdr82sh_sh1137_4sU_unstranded_UT

description: supplementary file: wdr82sh_4sU_unstranded_genes.fpkm_tracking.txt


title: wdr82sh_sh1137_4sU_unstranded_LPS_2h

value: LPS (10 ng/ml)


description:
wdr82sh_scrambled_total_stranded_UT_rep1.exons_gr1.counts.txt.gz
wdr82sh_scrambled_total_stranded_UT_rep1.introns_gr2.counts.txt.gz
UCSC_mm9_genes_introns.gtf.gz
UCSC_mm9_genes_sicer.gtf.gz

value: Stranded (first-strand synthesis)


title: wdr82sh_LMP_4sU_stranded_UT


title: wdr82sh_sh1137_4sU_stranded_LPS_1h


title: wdr82sh_LMP_4sU_unstranded_LPS_2h


title: wdr82sh_LMP_4sU_unstranded_UT


title: wdr82sh_scrambled_4sU_stranded_LPS_45min_DRB_untreated

description: supplementary file: wdr82sh_4sU_stranded_DRB_genes.fpkm_tracking.txt


title: wdr82sh_sh1137_4sU_stranded_LPS_45min_DRB_treated


title: set1absh_scrambled_4sU_stranded_LPS_45min

description: supplementary file: set1absh_4sU_stranded_genes.fpkm_tracking.txt


title: set1absh_scrambled_4sU_stranded_UT


title: wdr82sh_LMP_4sU_unstranded_LPS_4h


title: wdr82sh_LMP_polyA_unstranded_UT


title: wdr82sh_LMP_4sU_stranded_LPS_1h


title: set1absh_sh_4sU_stranded_LPS_45min


title: wdr82sh_LMP_4sU_unstranded_LPS_45min


title: set1absh_sh_4sU_stranded_UT


title: wdr82sh_scrambled_4sU_stranded_LPS_45min_DRB_treated


title: wdr82sh_sh1137_4sU_unstranded_LPS_45min


title: BMDMs_UT_wdr82sh_sh1137_intergenic_sx_Lgals3

value: 5' of the Lgals3 gene


title: pnutssh_scrambled_4sU_stranded_LPS_45min

description: supplementary file: pnutssh_4sU_stranded_genes.fpkm_tracking.txt


title: pnutssh_scrambled_4sU_stranded_UT


title: wdr82sh_sh1137_polyA_unstranded_LPS_4h


title: pnutssh_sh_4sU_stranded_LPS_45min


title: wdr82sh_LMP_polyA_unstranded_LPS_4h


title: BMDMs_HiC_biological_replicate_1

data_processing:
Library strategy: HiC-Seq
Reads were quality filtered according to the Illumina pipeline
The two ends of each paired-end sequenced fragment were separately aligned to the mm9 genome using NovoAlign (http://novocraft.com) (-s 2 -l 40)
Scripts provided with HOMER (PMID: 20513432) were used HiC data processing. As a first step, the makeTagDirectory script was run with the following parameters: restrictionSite AAGCTT -removeSelfLigation -removePEbg -genome mm9 -removeSpikes 10000 5. Then a background model considering a 40 kbps window was generated with the analyzeHiC script, using the following parameters: -res 40000 -bgonly
Locations of topologically associated domains (TADs) were computed using the scripts provided by Dixon et al. 2012 (PMID: 22495300)
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: The archive BMDMs_UT_HindIII.noSelfLigation.raw.tgz contains one file per chromosome showing the matrix of cis-interactions among all pairs of 40 kbps bins. BMDMs_UT_HindIII.noSelfLigation.raw.TADs.bed contains the coordinates of TADs.

growth_protocol: At day zero bone marrow cells were isolated from C57BL/6 mice and 1,5 × 10^6 cells/plate were seeded in 10 cm dishes in 10 ml of TET-free BM medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol:
Hi-C experiment were conducted in biological replicates using HindIII, according to the protocol published by Belton JM. Et al. Methods 2012 (PMID: 22652625) except for using 2% formaldehyde.
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Belton JM. Et al. Methods 2012 (PMID: 22652625).

tag: restriction enzyme

value: HindIII


title: BMDMs_HiC_biological_replicate_2


title: wdr82sh_sh1137_polII_total_UT

description: Chromatin IP against polII total

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID: 18798982) with default parameters. Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

extract_protocol:
Roughly 10-20 x 10^6 (for histone modifications) or 100-150 x 10^6 (for Pol II) fixed (1% formaldehyde for 10 min) macrophages were lysed with RIPA buffer and, after chromatin shearing by sonication.  Antibodies were pre-bound overnight to 100 ul of protein G-coupled paramagnetic beads (Dynabeads) in PBS/BSA 0.5%. Beads were then added to lysates and immunoprecipitation was let to proceed overnight. For Ser2-phospho RNA Pol II the ChIP lysates were incubated overnight with the primary antibody and then combined with 100 μl of beads that had previously been coupled overnight with 5 μg of rabbit anti-rat IgG (Jackson ImmunoResearch, #312-005-003). Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50 mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen).
Library preparation for Illumina sequencing (HiSeq 2000) was carried out using a described protocol (Garber et al., 2012) with slight modifications (Ostuni et al., 2013). The purified DNA libraries were quantified both with a 2100 Bioanalyzer (Agilent Technologies) and Qubit (LifeTechnologies) and diluted to a working concentration of 10 nM.

value: anti-Pol II (Santa Cruz, sc-899)

tag: retroviral infection


title: wdr82sh_sh1137_polII_total_LPS_45min

description: Chromatin IP against polII total

tag: cell type


title: pnutssh_sh_4sU_stranded_UT


title: wdr82sh_sh1137_polII_ser2P_UT

description: Chromatin IP against polII ser2P

value: anti-Ser2 Pol II (Chromotek, 3E10)


title: wdr82sh_sh1137_H3K4me3_UT

description: Chromatin IP against H3K4me3

value: FVB/Hsd

value: anti-H3K4me3 (Active Motif, #39159)


title: wdr82sh_sh1137_polII_ser2P_LPS_45min

description: Chromatin IP against polII ser2P


title: wdr82sh_sh1137_H3K4me1_LPS_45min

description: Chromatin IP against H3K4me1

value: anti-H3K4me1 (Abcam, ab8895)


title: wdr82sh_sh1137_H3K4me1_UT

description: Chromatin IP against H3K4me1


title: wdr82sh_sh1137_H3K27ac_UT

description: Chromatin IP against H3K27ac

value: anti-H3K27ac (Abcam, ab4729)


title: wdr82sh_sh1137_H3K36me3_LPS_45min

description: Chromatin IP against H3K36me3

value: anti-H3K36me3 (Abcam, ab9050)


title: wdr82sh_scrambled_H3K36me3_UT

description: Chromatin IP against H3K36me3

value: scrambled


title: wdr82sh_scrambled_polII_total_UT

description: Chromatin IP against polII total


title: wdr82sh_sh1137_H3K27ac_LPS_4h

description: Chromatin IP against H3K27ac


title: wdr82sh_scrambled_polII_ser2P_LPS_45min

description: Chromatin IP against polII ser2P


title: wdr82sh_scrambled_H3K4me1_LPS_45min

description: Chromatin IP against H3K4me1


title: wdr82sh_scrambled_polII_ser2P_UT

description: Chromatin IP against polII ser2P


title: wdr82sh_scrambled_H3K36me3_LPS_45min

description: Chromatin IP against H3K36me3


title: wdr82sh_scrambled_H3K4me1_UT

description: Chromatin IP against H3K4me1


title: H3K27me3_ChIPSeq_KitPlus

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet --solexa1.3-quals
Peak calling was done using MACS 2.0.9 with the following configurations: -q 1e-5 --llocal=10000 --bw 300 -m 5,30  --slocal=1000  -B  --keep-dup=1
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were automatically generated as an output of MACS 2.0.9; useq files were generated as part of the USeq software collection ChIPseq pipeline. Values in useq represent the Log2Ratio of the ChIP signal.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

value: postnatal day 7

tag: tissue

value: Testis

value: Spermatogonia

tag: chip antibody

tag: chip antibody vendor

value: Upstate

tag: chip antibody cat. #


title: H3K4me3_ChIPSeq_KitPlus

tag: age

value: Active Motif


title: Jun_4C_BMDMs_UT

data_processing:
Library strategy: 4C-seq
Reads were quality filtered according to the Illumina pipeline
Reads for different viewpoints were demultiplexed using fastq-multx (part of http://code.google.com/p/ea-utils)
4Cseqpipe (van de Werken et al. 2012) was used to map the reads and compute local coverage around viewpoints
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *.nearcis.cover.txt (refer to the 4Cseqpipe manual for full details about the format http://compgenomics.weizmann.ac.il/tanay/?page_id=367). 4Cseqpipe cis-profile around viewpoint.

value: BMDM cells (7th day of differentiation)


title: wdr82sh_LMP_H3K27ac_LPS_4h

description: Chromatin IP against H3K27ac

value: empty (LMP)

tag: treatment

value: LPS (10 ng/ml)


title: wdr82sh_LMP_H3K4me3_LPS_4h

description: Chromatin IP against H3K4me3

tag: strain


title: Ccl2_4C_BMDMs_UT


title: wdr82sh_LMP_H3K27ac_UT

description: Chromatin IP against H3K27ac

value: No treatment


title: wdr82sh_LMP_H3K4me3_UT

description: Chromatin IP against H3K4me3


title: Input_ChIPSeq_KitPlus


title: wdr82sh_sh1137_H3K36me3_UT

description: Chromatin IP against H3K36me3


title: H3K27me3_ChIPSeq_KitMinus


title: H3K4me3_ChIPSeq_KitMinus


title: Input_ChIPSeq_KitMinus


title: wdr82sh_sh1137_H3K4me3_LPS_4h

description: Chromatin IP against H3K4me3


title: D7_Thy1_BiSeq

data_processing:
Basecalls performed using CASAVA
Bisulfite reads were aligned using Novocraft novoalign in bisulfite mode with the following parameters: [-o SAM -rRandom -t240 -h120 -b2]
All downstream analysis and file manipulation were done using the USeq (http://useq.sourceforge.net/) suite.
Genome_build: mm9
Supplementary_files_format_and_content: Point methylation data files generated by useq viewable on IGB browser

extract_protocol:
DNA was extracted using Gentra PUREGENE DNA Isolation Kit and sheared on COVARIS to a median 400 bp fragment.
For all samples unmethylated lambda DNA was added to 1% final concentration (Promega Madison, WI 53711). Methylated paired-end adapters were ligated to sheared DNA according to the Illumina library preparation protocol. Sodium bisulfite conversion was performed using the EpiTect Bisulfite Kit (Qiagen, Valencia, CA 91355) with an additional incubation step at 60C for 120 min to increase conversion rate. Bisulfite treated DNA was then PCR amplified with 16 cycles and sequenced. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.


title: D0_Thy1_BiSeq

value: postnatal day 0


title: D7_KitMinus_BiSeq


title: D12_Thy1_BiSeq

value: postnatal day 12


title: D14_Kit_BiSeq

value: postnatal day 14


title: D7_Kit_BiSeq


title: D12_Kit_BiSeq


title: P7_Kit_Rep2

tag: cell markers

value: Kit


title: P7_Kit_Rep1


title: P12_Thy1_Rep1


title: P12_Kit_Rep1


title: P12_Kit_Rep2


title: P7_Thy1_Rep2


title: P12_Thy1_Rep2


title: P14_Kit_Rep1


title: D14_Thy1_BiSeq


title: P14_Thy1_Rep1


title: H4K20me1 N2 L3 Rep2 spike-in ChIPSeq

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.0.1 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Spike-in data was mapped to both the C. elegans genome and the C. briggsae genome build cb4. Reads mapping to both genomes were removed from further analysis.
Peaks were called using MACS version 1.4.2 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks per subunits, reads from the replicates were combined using the samtools utility merge version 0.1.19, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
Genome_build: WS220
Supplementary_files_format_and_content: Wig files were generated using MACS version 1.4.2, normalized according to the genome-wide mean coverage and the input subtracted. Scores represent the average coverage of each replicate at each base position.  Bed files were generated by combining replicate reads and using MACS version 1.4.2 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.

organism: Caenorhabditis elegans

growth_protocol: L3s were isolated by growing hatched L1 larvae on OP50 seeded NGM plates for 24 hours at 20C temperature.

extract_protocol:
Frozen, ground, and crosslinked larva samples were resuspended in FA buffer+sarkosyl+protease inhibitors (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl, 0.1% sarkosyl), and sonicated to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of extract was spiked in with 0.1-0.2 mg of C. Briggsae AF16 extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA and 10-20 ng of input DNA were ligated to Illumina multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: L3 collections were made by freezing worms in liquid nitrogen, then were ground into a frozen powder, then treated with 1% formaldehyde for 10 minutes, washed with M9, and collected by centifugation for extract preparation.

tag: developmental stage

tag: matching input

value: H4K20me1 Abcam (ab9051)


title: MK4 L1 Rep3 RNAseq

description:
mRNA
RNAseq_FPKMs.txt


title: P0_Thy1_Rep1


title: P0_Thy1_Rep2


title: MK4 L1 Rep2 RNAseq

description:
mRNA
RNAseq_FPKMs.txt


title: BS553 L3 Rep2 RNAseq

description:
mRNA
RNAseq_FPKMs.txt


title: BS553 L3 Rep3 RNAseq

description:
mRNA
RNAseq_FPKMs.txt


title: MK4 L1 Rep1 RNAseq

description:
mRNA
RNAseq_FPKMs.txt


title: BS553 L3 Rep1 RNAseq

description:
mRNA
RNAseq_FPKMs.txt


title: Input_N2_L3_spikein_Rep2

value: none (input)