title: HepG2 total RNA miR-497

city: Tokyo

first: Johji

last: Inazawa

address: 1-5-45 Yushima, Bunkyo-ku

institute: Tokyo Medical & Dental University

description: total RNA

data_processing:
Basecalls performed using CASAVA version 1.7
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using runRNA.pl (included in CASAVA version 1.7). RPKM data files from each chromosome were merged into one tab-delimited text file.
Genome_build: hg19
Supplementary_files_format_and_content: Fastq files were generated using CASAVA version 1.7.  Tab-delimited text files include RPKM values were generated using runRNA.pl for each sample.

source_name: HepG2,miR-497,24h, totalRNA

growth_protocol: Hep G2 were maintained in appropriate media, D-MEM medium supplemented with 10%fetal bovine serum.

extract_protocol:
Ago2-IP RNA containing lysates from the immunopriticipation, RNA fractions were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. The protocol includes clean up step after DNaseI (TaKaRa, Shiga, Japan) digestion. RNAs were quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using TrueSeq mRNAvSample Preparation Kit, Set A with standard Illumina protocol, TrueSeq RNA Sample Preparation Guide (November 2010).

treatment_protocol: Cells were transfected with or without 5 nM of miCENTURY OC miNatural mimicking miR-195 or miR-497(COSMO BIO, Tokyo, Japan) using Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA) . 24hours after transfection, Immunopriticipation with anti-human Argonute 2 was performed using microRNA Isolation Kit, Human Ago2 (Wako, Pure Chemical, Osaka, Japan) according to the manufacturer's instructions.

tag: cell line

tag: time


title: HepG2 Ago2IP miR-497

status: Public on May 31 2013

type: SRA

country: Japan

description: Ago2-IP RNA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: HepG2,miR-497,24h, Ago2-IP

tag: antibody

tag: antibody manufacturer

value: Wako

tag: treatment


title: HepG2 total RNA NT

description: total RNA

value: NT

value: 0 h


title: HepG2 Ago2IP NT

description: Ago2-IP RNA


title: HepG2 total RNA miR-195

description: total RNA

source_name: HepG2,miR-195,24h, totalRNA


title: HepG2 Ago2IP miR-195

description: Ago2-IP RNA

source_name: HepG2,miR-195,24h, Ago2-IP


title: rde-1_1

status: Public on Jun 01 2013

city: Cambridge

first: Eric

middle: A.

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

country: United Kingdom

institute: University of Cambridge

data_processing:
Adaptors were removed with Cutadapt ver 1.0
Fastq files were converted to fasta files using a custom perl script run in Perl version 5.8.12
Fasta files were collapsed using FastX toolkit
Collapsed fasta files were trimmed so that only reads with length of 15 nucleotides or above were included, using a custom perl script run in Perl version 5.8.12
Supplementary_files_format_and_content: collapsed fasta files with adaptors removed with the header sequence number-read count_sequence

organism: Caenorhabditis elegans

source_name: C.elegans whole animal, Orsay virus infected, mixed stage

growth_protocol: C. elegans were grown under standard conditions at 20C The food source used was E. coli strain HB101 (Caenorhabditis Genetics Center, University of Minnesota, Twin Cities, MN, USA). Uninfected animals were picked as L4s and virus laid onto the plates after 24hrs.

extract_protocol: cDNA libraries were prepared from total RNA using the Illumina Truseq protocol according to the manufacturer's instructions.

treatment_protocol: RNA was extracted from worms 4 days after infection with the Orsay virus using Trizol.

tag: 5' end dependence

value: 5' Independent (RNA treated with 5' RNA polyphosphatase (Epicentre) for 30 minutes at 37C)

tag: genotype

value: rde-1 ne219

tag: tissue

value: whole animal


title: AP4_ChIP_DOX

city: Munich

first: Rene

last: Jackstadt

address: Thalkirchnerstrasse 36

country: Germany

institute: Ludwigs maximilians University Munich

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Eland.
Peak-calling was performed using FindPeaks applying a cut-off set at a minimum of 6 overlapping reads considering bidirectional enrichment.
Genome_build: hg19

molecule: genomic DNA

source_name: Colorectal cancer cells

growth_protocol: DLD-1 cells and their derivatives were cultured in McCoy´s grwoth Medium containig 10% FBS at 37°C and 5%CO2.

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 Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Before cross-linking DLD-1 cells were treated with DOX (100 ng/ml) for 24 hours to induce ectopic expression of AP4.

value: TFAP4, HPA001912, Sigma


title: PL5

city: Stanford

first: Craig

middle: Patrick

last: Giacomini

state: CA

address: 269 Campus Drive (CCSR 3245A)

department: Pathology

country: USA

institute: Stanford University

data_processing:
Samples were mapped to the human genome and RefSeq transcriptome using ELAND.
A custom C# script was used to extract all mate pairs with one read mapping to the candidate rearranged gene (identified by breakpoint analysis) and the other read mapping to a separate genomic locus.
A separate C# script screened mate pairs for single reads mapping to potential exon-exon fusion junctions of nominated gene fusions.
Genome_build: hg18
Supplementary_files_format_and_content: Our pipeline outputs a single file (GeneFusions.txt) after all samples are run through our pipeline.  This file is a tab delimited text file with the first column representing the gene fusion name, the second column includes the sample from which the gene fusion was identified, the third column includes the chromosome of the 5' partner gene, the fourth column includes the chromosome of the 3' partner gene, the fifth column includes the exon position of the gene fusion junction, and the sixth column includes the number of mate pairs supporting the specific gene fusion.

source_name: Pancreatic cancer cell line

growth_protocol: Cell lines were cultured in RPMI + 10% FBS until 60-70% confluent.  Total RNA was then harvested using the Rneasy Mini Kit (Qiagen)

extract_protocol: mRNA Seq-8 Sample Prep Kit (Illumina)

treatment_protocol: No treatment performed

tag: cancer subtype

value: pancreatic cancer


title: HCC1954

source_name: Breast cancer cell line

value: breast cancer


title: BT-549


title: WT_2a2

city: Cleveland

first: Donny

middle: D

last: Licatalosi

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve University

description: brain 2, sample 2

data_processing:
Library strategy: HITS-CLIP
base calling
collapse duplicate reads
initial mapping to mouse genome mm8 with bowtie
eliminate reads mapping to multiple genomic loci
pooling of reads from individual samples
conversion of mm8 to mm9 with LiftOver
Genome_build: mm9
Supplementary_files_format_and_content: All processed data from each sample was combined into two files, a single BED file and a single WIGGLE file.  The BED file contains color-coded information to distinguish each technical and biologic replicate, as well as sample IDs.  For example "1a1, 1a2, 1b1,and 1b2" corresponds to four HITS-CLIP libraries derived from the cortex of animal 1.  The WIGGLE file contains CLIP tag density per nucleotide (i.e., number of CLIP tags per nucleotide of genomic sequence).  For both the BED and WIGGLE files, the datasets are separated into two tracks for each strand (ie., each file when uploaded in the UCSC genome browser will appear as two separate tracks, one for each strand).

organism: Mus musculus

source_name: embryonic cortex

growth_protocol: Animals (CD1 strain) housed and timed matings performed following standard procedures.  Day when copulatory plug is observed is considered embryonic day 0.5.  Embryos collected at day 18.5 by caesarian section.

extract_protocol:
Sample preparation and library construction as described in Licatalosi et al., 2012 (PMID: 22802532)
First five nucleotides of each sequence are: NNNNG, where N are degenerate bases followed by a G.

value: cortex

tag: strain

value: CD1 strain

tag: developmental stage

value: embryonic day 18.5 (E18.5)

tag: rna subtype

value: RNA crosslinked to Ptbp2


title: WT_1b2

description: brain 1, sample 4


title: WT_2b2

description: brain 2, sample 4


title: WT_1b1

description: brain 1, sample 3


title: WT_2b1

description: brain 2, sample 3


title: WT_2a1

description: brain 2, sample 1


title: HEA-7

city: Hamilton

first: Turlough

middle: M

last: Finan

state: Ontario

address: 1280 Main Street West

department: Biology

country: Canada

institute: McMaster University

data_processing:
Two independent cDNA runs from each of the two RNA samples (P0 and P2) were pooled to give RNA sequence reads that were aligned by matching the 34 nucleotide sequence of the read to the S. meliloti genome.
34 nucleotide reads were aligned against a file of all 34-mers (+ and - strands) from the S. meliloti genome using a hash table and a program writted in C.
The DNA sequences for the 34-mer table were taken from NCBI genbank files: AL591985, AL591688, AE006469
The first pass found perfect matches (PM), a second found single mismatched reads (MM1) and a third pass matched the remaing reads to the S. meliloti genome by Blast (BM). The file SmP_summary contains summary information about the reads matched and unmatched.
Read counts were multiplicity corrected by dividing by the number of times the 34-mer appeared in the S. meliloti genome.
Pooled PM read counts for P0 and P2 were normalized: P0 (multiplied by 1.026) and P2 (1.057) so that the total number of normalized, perfectly matched read counts for each experiment would be 10,000,000.
Supplementary_files_format_and_content: Three files (chromosome, pSymA, pSymB) contained the multiplicity corrected, normalized nymber of directionally matched PM reads by genome position (see processed_data_readme.txt).

organism: Sinorhizobium meliloti

source_name: Cell culture

growth_protocol: S. meliloti RmP110 strain cultures were grown in LB medium containing 2.5mM MgSO4 and 2.5mM CaCl2 (LBmc). Subcultured in phosphate-free MOPS-buffered minimal medium (MOPS-P0 (17)), contained 40 mM MOPS pH 7.4 with KOH, 20 mM NH4Cl, 100 mM NaCl, 1.2 mM CaCl2, 2 mM MgSO4, with 0.3 µg ml -1 biotin, 10 ng ml-1 CoCl2, 15 mM glucose as carbon source and trace minerals (22). Phosphate rich medium, MOPS-P2 was MOPS-P0 with K2HPO4 at a final concentration of 2 mM.

extract_protocol: A directional mRNA-sequence library was prepared following Illumina's protocol. Briefly, RNA samples were prepared as described above and Zn-treated for fragmentation. Specific primers were added, first to the 3' end and then to the 5’ end of RNA fragments by single-stranded ligation. cDNA was then synthesized using a primer complementing the 3' adapter and the final library was obtained by PCR using two primers that complement the flanking adapter sequences. The library preparation and Illumina sequence reads of 34 nucleotides was performed by FASTERIS SA (Geneva, Switzerland).

treatment_protocol: RNA was prepared from S. meliloti grown in MOPS minimal media containing 20 µM (MOPS-P0) or 2 mM (MOPS-P2) inorganic phosphate respectively.   Total RNA was isolated using the hot-phenol method; DNase I treated and cleaned using Qiagen RNeasy mini columns. rRNA was removed via two purifications using the Ambion MicrobExpress Bacterial mRNA Enrichment kit.

tag: culture conditions

value: P0:MOPS + 20 µM Pi

tag: growth phase

value: Exponential phase


title: WT_1a2

description: brain 1, sample 2


title: Neural progenitor cells+GFP knockdown+FBS(1%/6hr) rep

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

institute: Max Delbrüch Center

data_processing:
FPKM from tag density files and genomeCoverageBed
Genome_build: Ensembl and RefSeq genes
Supplementary_files_format_and_content: FPKM

source_name: Sub-ventricular zone (brain)

extract_protocol: PCR amplification

value: GFP knockdown+FBS(1%/6hr)

value: FVB

tag: cell type

value: Sub ventricular-zone derived neural stem cells

value: Ink4a/Arf -/-;BMI1 dox-inducible shRNA


title: Neural progenitor cells+GFP knockdown+FBS(1%/3hr) rep

value: GFP knockdown+FBS(1%/3hr)


title: Neural progenitor cells+GFP knockdown+BMP4(10ng/6hr) rep2

value: GFP knockdown+BMP4(10ng/6hr)


title: SUPT13

source_name: T-ALL cell line

value: T-ALL


title: Neural progenitor cells+GFP knockdown+BMP4(50ng/6hr) rep

value: GFP knockdown+BMP4(50ng/6hr)


title: Neural progenitor cells+GFP knockdown+BMP4(10ng/3hr) rep

value: GFP knockdown+BMP4(10ng/3hr)


title: Neural progenitor cells+GFP knockdown+BMP4(10ng/6hr) rep


title: Neural progenitor cells+GFP knockdown+FBS(10%/6hr) rep

value: GFP knockdown+FBS(10%/6hr)


title: Neural progenitor cells (control 1)


title: Neural progenitor cells (control 2)


title: Neural progenitor cells+BMI1 knockdown+FBS(1%/6hr)

value: BMI1 knockdown+FBS(1%/6hr)


title: Neural progenitor cells+GFP knockdown+BMP4(50ng/3hr) rep

value: GFP knockdown+BMP4(50ng/3hr)


title: Neural progenitor cells+BMI1 knockdown+FBS(10%/3hr)

value: BMI1 knockdown+FBS(10%/3hr)


title: Neural progenitor cells+BMI1 knockdown+FBS(1%/3hr)

value: BMI1 knockdown+FBS(1%/3hr)


title: Neural progenitor cells+BMI1 knockdown+BMP4(50ng/3hr)

value: BMI1 knockdown+BMP4(50ng/3hr)


title: Neural progenitor cells+BMI1 knockdown+BMP4(50ng/6hr)

value: BMI1 knockdown+BMP4(50ng/6hr)


title: WT_1a1

description: brain 1, sample 1

value: cortex

value: CD1 strain

value: embryonic day 18.5 (E18.5)

value: RNA crosslinked to Ptbp2


title: Bmi1-/- whole brain RNA-seq_1

source_name: whole brain

value: FVB

value: brain


title: Neural progenitor cells+BMI1 knockdown+BMP4(10ng/3hr)

value: BMI1 knockdown+BMP4(10ng/3hr)

value: Sub ventricular-zone derived neural stem cells

value: Ink4a/Arf -/-;BMI1 dox-inducible shRNA


title: Bmi1-/- whole brain RNA-seq_2


title: Wild-type whole brain RNA-seq_2


title: Neural progenitor cells+BMI1 knockdown+FBS(10%/6hr)

value: BMI1 knockdown+FBS(10%/6hr)


title: Wild-type whole brain RNA-seq_1


title: Neural progenitor cells+GFP knockdown+BMP4(10ng/3hr) rep2

value: GFP knockdown+BMP4(10ng/3hr)


title: expanded FOXP3-losing H3K27me3

city: Xi'an

first: Haiqi

last: He

state: Shaanxi

address: West Yanta Road

country: China

institute: Xi'an Jiaotong University

description: Sample 4

data_processing:
Base-calling was performed using RTA and the data was transformed with OLB version 1.9.0.
Raw data were filtered using the following specifications. The adaptor sequence and low-quality sequence were removed. The low-quality read was defined as sequence whose Q20 ≥50%, or that contains more than 10% unkown base N.
Clean reads were mapped to the hg19 using SOAP version 2.21 with parameters -p 4 -l 23 -v 2 -s 35. Only alignments with ≤2 mismatching bases were retained.
Peaks were identified using MACS version 1.4.0 with default parameters.
Genome_build: UCSC human genome (hg19)
Supplementary_files_format_and_content: wig file

source_name: CD4+CD25highCD127low/- Treg cells

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation from leukapheresis products of healthy volunteers. CD4+ T cells were enriched with the human CD4+ T Cell Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). CD4+CD25highCD127low/- Treg cells were isolated by FACS (BD Biosciences, USA) from enriched CD4+ T cells and cultured in X-Vivo 15 medium (Lonza, USA) supplemented with 5% human AB serum (Sigma-Aldrich, USA). Cells were stimulated with anti-CD3/CD28 Abs-coated beads (Invitrogen-Dynal, USA) in the presence of 500 U/ml recombinant human IL-2 (PeproTech, USA) for 8 days and then rested in the presence of 100 U/ml IL-2 for 14 days. After two cycles of stimulation, cells were rested for 4-5 days.

extract_protocol:
Cells were crosslinked with 1% formaldehyde and chromatin was sonicated to obtain an average fragment length of 200 to 500 bp. After preclearing with protein A agarose beads (Upstate, USA), sonicated chromatin was precipitated with anti-H3K4m3 and anti-H3K27m3 (abcam, United Kingdom) overnight at 4℃. The immune complexes were bound to protein A agarose beads (Upstate, USA). After washing and elution, crosslinks were reversed at 65℃ overnight. The eluted DNA was treated sequentially with Proteinase K and RNase A, and purified with the QIAquick PCR-purification kit (Qiagen, Germany). The enrichment efficiency of ChIP was detected using qPCR approach.
The purified DNA fragments was repaired using PNK and Klenow enzyme, and ligated to adapters.  Subsequently, PCR-amplified fragments of around 100-300bp were sequenced using Illumina HiSeq™ 2000 following manufacturer’s protocols (www.illumina.com).

treatment_protocol: Expanded cells were sorted into FOXP3+ and FOXP3-losing cells by FACS (BD Biosciences, USA). For intracellular staining, washing and following cell sorting steps, the PBS with 0.1% diethyl pyrocarbonate (DEPC; Sigma-Aldrich, USA) was used. The buffer was autoclaved and supplemented with recombinant RNasin® Ribonuclease Inhibitor (Promega, USA) just before use.

tag: cell type origin

value: CD4+CD25highCD127low/- Treg

tag: cell subtype

value: expanded human FOXP3-losing Treg cells

tag: days of expansion

tag: foxp3 status

value: negative

tag: chip antibody

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: Neural progenitor cells+GFP knockdown+FBS(10%/3hr) rep

tag: treatment

value: GFP knockdown+FBS(10%/3hr)

tag: genotype


title: expanded FOXP3-losing H3K4me3

description: Sample 3

value: Peripheral blood mononuclear cells (PBMC)


title: expanded FOXP3+ H3K4me3

description: Sample 1

value: expanded human FOXP3+ Treg cells

value: positive


title: Multi_B

source_name: Combined cancer cell lines (SUPT7, ONS76, SH-4)

tag: cell line

value: SUPT7, ONS76, SH-4

tag: cancer subtype

value: SUPT7-TALL, ONS76-GBM, SH-4-melanoma


title: Multi_A

source_name: Combined cancer cell lines (A172, A431, D538MG)

value: A172-GBM, A431-epidermoid carcinoma, D538MG-anaplastic astrocytoma


title: Multi_C

source_name: Combined human cancer cell lines (CHL-1, DKMG, JURKAT)

value: CHL-1, DKMG, JURKAT

value: CHL-1-melanoma, DKMG-GBM, JURKAT-TALL


title: N2_2

tag: 5' end dependence

value: 5' Independent (RNA treated with 5' RNA polyphosphatase (Epicentre) for 30 minutes at 37C)

value: N2 (Bristol)

tag: tissue

value: whole animal


title: wild-type w/o fluconazole

city: Anseong

first: Jeongmi

last: Kim

address: 4726 Seodong-daero

department: Dept. of Biotechnology

country: South Korea

institute: Chung-Ang University

description: wild-type w/o fluconazole

data_processing:
Base-calling: CASAVA v1.6
Alignment: CLC Genomics Workbench 4.5
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
Genome_build: Cryptococcus neoformans var. grubii H99 Sequencing Project, Broad Institute of Harvard and MIT (http://www.broadinstitute.org/)
Supplementary_files_format_and_content: rpkm

organism: Cryptococcus neoformans H99

source_name: Cryptococcus neoformans var. grubii H99

growth_protocol: Wild-type and cfo1 mutants were grown in YPD overnight at 30℃. Cells were diluted to 1.0ｘ106 cells in 50 ml YPD medium without 10 ug/ml of fluconazole(dissolved in DMSO). DMSO was added to YPD medium without fluconazole sample as a drug-free control. Cultures were incubated with shaking at 30℃ for 3 hours and harvested for RNA extraction.

extract_protocol: Total RNA was extracted with the RiboPure™-Yeast Kit (Ambion, AM1926) according to the manufacturer's instruction.

treatment_protocol: Each sample was treated with or without 10 ug/ml of fluconazole for 3 hours.

value: wild-type

value: no fluconazole


title: wild-type w/ fluconazole

description: wild-type w/ fluconazole

growth_protocol: Wild-type and cfo1 mutants were grown in YPD overnight at 30℃. Cells were diluted to 1.0ｘ106 cells in 50 ml YPD medium with 10 ug/ml of fluconazole(dissolved in DMSO). Cultures were incubated with shaking at 30℃ for 3 hours and harvested for RNA extraction.

value: fluconazole


title: cfo1 w/ fluconazole

description: cfo1 w/ fluconazole


title: cfo1 w/o fluconazole

description: cfo1 w/o fluconazole


title: pitx(RNAi) animals 1

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

data_processing:
Base calls were made using the Illumina pipeline v. 1.6 for Illumina GAIIx and v. OLB 1.9 for HiSeq2000
All RNAseq was pooled and a de novo transcriptome was made using the program Trinity with default settings.
smed20110214_transcripts.nt transcriptome was deposited into NCBI TSA database
Triplicated experiments were analyzed by the program baySeq and resulting false discovery rate probabilities are provided in Table S1.
Genome_build: smed20110214_transcripts.nt
Supplementary_files_format_and_content: Table_S1.xls  Excel tab delimited
Supplementary_files_format_and_content: RPM quantification for all 3 RNAi conditions used in this study.  Sheet 1 is each control replicate vs. pitx(RNAi) and sheet 2 is each control replicate vs. lhx1/5-1(RNAi).  baySeq statistical analysis provided false discovery rate (FDR) p-values.
unc_1 control(RNAi) animals (unc22) 1
Unc_2 control(RNAi) animals (unc22) 2
Unc_3 control(RNAi) animals (unc22) 3
pitx_1 pitx(RNAi) animals 1
pitx_2 pitx(RNAi) animals 2
pitx_3 pitx(RNAi) animals 3
lhx_1 lhx1/5-1(RNAi) animals 1
lhx_2 lhx1/5-1(RNAi) animals 2
lhx_3 lhx1/5-1(RNAi) animals 3

organism: Schmidtea mediterranea

source_name: pitx(RNAi) animals

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to RNAi feeding, fed 5x, then collected 12 days later (5fd12).

extract_protocol: All 3 tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.

value: Whole worms, asexual CIW4


title: Neural progenitor cells+BMI1 knockdown+BMP4(10ng/6hr)

value: BMI1 knockdown+BMP4(10ng/6hr)

tag: strain

value: FVB

value: Sub ventricular-zone derived neural stem cells

value: Ink4a/Arf -/-;BMI1 dox-inducible shRNA


title: control(RNAi) animals (unc22) 2

source_name: control(RNAi) animals (unc22)


title: lhx1/5-1(RNAi) animals 2

source_name: lhx1/5-1(RNAi) animals


title: lhx1/5-1(RNAi) animals 3


title: control(RNAi) animals (unc22) 1


title: pitx(RNAi) animals 2


title: Condylura_DRG2

city: Berkeley

first: Maurizio

last: Pellegrino

address: 355 LSA

institute: University of California - Berkeley

description:
readcounts_cc.txt
DRG_Cc.txt
DRG_overlap.txt

data_processing:
Alignments were performed with Stampy v1.0.11 (substitution rate = 0.03). For Condylura sequences, the total read count was the sum of all reads aligning to the homologs of that gene in Homo sapiens, Canis familiaris, or Mus musculus (Entrez Gene database, ncbi.nlm.nih.gov, Jan 2011). Homology was based on the HomoloGene database (build 64) and manual annotation. For Mus sequences, only the Mus musculus transcriptome database was used.
Differential expression was assessed using the DESeq package for R, with a padj < 0.05
Genome_build: Homo sapiens transcriptome downloaded Nov 25th 2010 (genome.ucsc.edu). Canis lupus familiaris and Mus musculus transcriptomes downloaded Nov28th 2010, (ncbi.nlm.nih.gov)
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values and variance for each sample based on the analysis performed using DESeq
Supplementary_files_format_and_content: readcounts_cc.txt: Read counts for genes in Condylura cristata trigeminal and dorsal root ganglia
Supplementary_files_format_and_content: readcounts_mm.txt: Read counts for genes in Mus musculus trigeminal and dorsal root ganglia
Supplementary_files_format_and_content: TG_Cc.txt: Genes overexpressed in Condylura cristata trigeminal versus dorsal root ganglia
Supplementary_files_format_and_content: DRG_Cc.txt: Genes overexpressed in Condylura cristata dorsal root versus trigeminal ganglia
Supplementary_files_format_and_content: TG_overlap.txt: Set of genes overxpressed in both mouse and mole trigeminal versus dorsal root ganglia
Supplementary_files_format_and_content: DRG_overlap.txt: Set of genes overxpressed in both mouse and mole dorsal root versus trigeminal ganglia

organism: Condylura cristata

source_name: dorsal root ganglia

extract_protocol:
Tissues were removed and homogenized in Trizol (Invitrogen) as per the manufacturer’s instructions.
Illumina TruSeq RNA Sample Prep Kit was used with about 1 ug of total RNA for the construction of sequencing libraries. After poly-A mRNA selection, the first Condylura trigeminal and dorsal root ganglia samples (Condylura_TG1 and Condylura_DRG1) were retrotranscribed and the Illumina Genomic Sample Prep Kit was used to generate libraries. These were sequenced on a Genome Analyzer II (76 bp). The remaining Condylura and Mus samples were processed using the Illumina TruSeq kit, and libraries were sequenced on a HighSeq 2000 (36 bp or 50bp). WHICH ONES ON WHICH The Condylura samples are single reads, the Mus samples are paired-end.

value: dorsal root ganglia

tag: age

value: adult

tag: Sex

value: male

value: wild


title: Mus_DRG1

description:
readcounts_mm.txt
DRG_overlap.txt

value: female


title: Condylura_DRG1


title: Mus_TG3

description: The results presented in the manuscript for the mouse data are based on two mouse samples, so there is no processed data file.

source_name: trigeminal ganglia

value: trigeminal ganglia


title: Mus_DRG2

description:
readcounts_mm.txt
DRG_overlap.txt


title: Mus_DRG3


title: expanded FOXP3+ H3K27me3

description: Sample 2

tag: cell type origin

value: Peripheral blood mononuclear cells (PBMC)

tag: cell type

value: CD4+CD25highCD127low/- Treg

value: expanded human FOXP3+ Treg cells

value: positive

value: abcam


title: Condylura_TG3

description:
readcounts_cc.txt
TG_Cc.txt
TG_overlap.txt


title: Mus_TG2

description:
readcounts_mm.txt
TG_overlap.txt


title: pitx(RNAi) animals 3


title: control(RNAi) animals (unc22) 3


title: Condylura_TG1


title: Condylura_TG2


title: Mus_TG1

description:
readcounts_mm.txt
TG_overlap.txt


title: Female-24hr-Input

status: Public on May 30 2013

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

description: Input DNA (after preclear) for female embryonic stem cells differentiated with retinoic acid

data_processing:
Library strategy: RAP-Seq
Align: BWA version 0.5.9 with default parameters
Filter: Remove reads with mapping qualities less than 30 or if flagged as PCR duplicates for both read pairs by Picard
Count: Count read-pairs that overlap a given window in the genome
Normalize:  Divide read-pair count in a RAP experiment by the read-pair count in the input + 0.1
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files represent normalized enrichment ratios in windows across the genome.  Windows deemed "unmappable" are omitted (see Engreitz et al. 2013).  For the pSM33 timecourse, replicate Xist RAP experiments were combined to generate the final processed data.  For pSM33 timecourse and female ES timecourse, counts in the input files were also combined across time points.

source_name: F1 2-1 24hr retinoic acid

growth_protocol: Female ES cells were cultured in medium containing Knockout DMEM (Life Technologies) supplemented with 15% fetal calf serum (GlobalStem), 1X NEAA (Life Technologies), 2 mM L-glutamine (Life Technologies), 0.1 mM beta-mercaptoethanol (Sigma), with or without 1000U/mL LIF (GlobalStem) on a mitotically inactivated male MEF feeder layer. At the start of the experiment, the ES cells were passaged using 0.05% trypsin and pre-plated for 45 minutes in ES medium onto plates treated with 0.3% gelatin to deplete MEFs from the culture. ES cells were then collected and seeded onto plates coated with 0.3% gelatin at a density of 15K cells/cm2 and plated in in ES medium + 1000U/mL LIF. Cells were all cultured for 48 hours and all-trans retinoic acid (RA) (Sigma) was added at different time points. At each time point, medium was removed from the culture and replaced with ES medium lacking LIF and supplemented with freshly diluted 1uM RA.

extract_protocol:
RNA Antisense Purification (RAP) was performed as described in Engreitz et al. 2013
NEBNext ChIP-Seq Library Prep Kit

value: embryonic stem cell

tag: induction time

value: 24 hours

tag: experiment type

value: Input

tag: gender


title: Female-6hr-Xist

description: RAP-Seq using probes targeting Xist on female embryonic stem cells differentiated with retinoic acid

source_name: F1 2-1 6hr retinoic acid

value: 6 hours

value: Xist RAP


title: NoDox-Input

description: Input DNA (after preclear) for pSM33 male embryonic stem cells induced with doxycycline

source_name: pSM33 0hr dox

growth_protocol: Male ES cells were grown on plates coated with 0.2% gelatin in serum-free 2i/LIF media composed as follows:  1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).  Xist expression was induced by adding 2 micrograms per milliliter (ug/mL) doxycycline at a defined time before harvesting cells.

value: 0 hours


title: Female-48hr-Input

source_name: F1 2-1 48hr retinoic acid

value: 48 hours


title: Female-24hr-Xist


title: 0hr-Washout-Xist

description: RAP-Seq using probes targeting Xist on pSM33 male embryonic stem cells induced with doxycycline

source_name: pSM33 1hr dox

value: 1 hour


title: 1hr-Washout-Xist

source_name: pSM33 1hr dox 1hr wash

growth_protocol: Male ES cells were grown on plates coated with 0.2% gelatin in serum-free 2i/LIF media composed as follows:  1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).  Xist expression was induced by adding 2 micrograms per milliliter (ug/mL) doxycycline for one hour.  Then the dox-containing medium was replaced with fresh medium for one hour before cells were harvested.

value: 1 hour and 1 hour wash-out

value: male


title: Female-6hr-Input

value: female


title: Female-3hr-Xist

source_name: F1 2-1 3hr retinoic acid

value: 3 hours


title: Female-48hr-Xist


title: Female-0hr-Input

source_name: F1 2-1 0hr retinoic acid

value: 0 hour


title: Female-3hr-Input


title: 0hr-Washout-Input


title: NoDox-Xist


title: delSXC9-Input

description: Input DNA (after preclear) for delSXC9 male embryonic stem cells induced with doxycycline

source_name: delSXC9 3hr dox


title: delSXC9-Xist

description: RAP-Seq using probes targeting Xist on delSXC9 male embryonic stem cells induced with doxycycline


title: pSM33-6hr-Input

description: Input DNA (after preclear) for  pSM33 male embryonic stem cells induced with doxycycline

source_name: pSM33 6hr dox


title: pSM33-3hr-Input

source_name: pSM33 3hr dox


title: MLF-ControlSense

description: RAP-Seq using probes with the same strand as Xist on female mouse lung fibroblasts

source_name: MLF

growth_protocol: MLFs were grown in DMEM High Glucose (Life Technologies) + 10% fetal calf serum (GlobalStem)

value: MLF

value: mouse lung fibroblast

value: not applicable

value: Xist Sense Control RAP


title: delXF6-Xist

description: RAP-Seq using probes targeting Xist on delXF6 male embryonic stem cells induced with doxycycline

source_name: delXF6 3hr dox

value: embryonic stem cell


title: MLF-Input

description: Input DNA (after preclear) for female mouse lung fibroblasts


title: lhx1/5-1(RNAi) animals 1

value: Whole worms, asexual CIW4


title: MLF-Xist

description: RAP-Seq using probes targeting Xist on female mouse lung fibroblasts


title: Female-0hr-Xist


title: 1hr-Washout-Input

value: Input


title: pSM33-0hr-Input


title: pSM33-2hr-Input

source_name: pSM33 2hr dox

value: 2 hours


title: pSM33-6hr-Xist-R2

value: 6 hours

value: Xist RAP


title: pSM33-3hr-Xist-R2


title: pSM33-2hr-Xist-R2


title: pSM33-1hr-Xist-R2


title: pSM33-0hr-Xist-R2

value: 0 hours


title: pSM33-6hr-Xist-R1


title: pSM33-1hr-Xist-R1

value: 1 hour


title: pSM33-2hr-Xist-R1


title: pSM33-0hr-Xist-R1


title: PGC_H3K4me3_ChIPSeq

city: San Francisco

first: Courtney

last: Onodera

address: 1450 Third St, HD374

institute: University of California, San Francisco

description:
Chromatin IP against H3K4me3 (Diagenode pAb003-050, lot # A5051-001P)
This Sample represents 2 replicates.

data_processing:
Reads from each ChIP-Seq library were filtered to retain only unique sequences. Fiitered reads were aligned to the mm9/NCBI build 37 mouse genome using bowtie (v0.12.7) and reads mapping only once were retained.
A 13-state segmentation of the genome was generated using ChromHMM (v1.06) to call and compare H3K4me3- and H3K27me3-enriched regions in PGCs and ESCs (ESC data obtained from GEO accession GSE12241 and handled in the same manner as PGC data). The four samples (PGC H3K4me3, PGC H3K27me3, ESC H3K4me3, ESC H3K27me3) were treated as distinct marks from a single cell type to allow a direct and unbiased comparison of the genome segmentation in PGCs and ESCs. K-means clustering was used to group the state emission parameters for each sample into 2 groups ("on" or "off"), and these were used to classify each of the 13 ChromHMM segmentation states as "bivalent", "H3K4me3 only", "H3K27me3 only", or "none" for each cell type. Data from the replicate PGC libraries were pooled together for this analysis. H3 ChIP-Seq data from the ESC dataset (GEO accession GSE12241) was used as control for the ESC samples.
All genomic segments from the ChromHMM PGC H3K4me3- or PGC H3K27me3-containing ("on") states were merged into summary bed files.
Genome_build: MGSCv37
Supplementary_files_format_and_content: All files in UCSC BED format.

source_name: E11.5 Primordial Germ Cells, H3K4me3 ChIP

growth_protocol: We used a transgenic Oct4:GFP B6 mouse line crossed to Swiss-Webster females. The gonadal regions from multiple embryos were isolated at E11.5 and pooled prior to enzymatic dissociation. Primordial germ cells (PGCs) were isolated by FACS as the GFP+ population.

extract_protocol:
Two aliquots of E11.5 PGCs, consisting of 104,000 and 97,000 cells, were cross-linked in 0.25% formaldehyde (Thermo Scientific 28906) in PBS for 10min at room temperature prior to quenching with 125mM glycine. Cross-linked material was sonicated using a Covaris sonicator for 12' at Duty 5%, Intensity 3, and Bursts 200. Lysate for each replicate was diluted in lysis buffer and cleared of debris. Cleared lysate from each replicate was divided equally to perform ChIP for H3K4me3, H3K27me3, and an input control. For each IP, 11µl of protein A Dynabeads (Life Technologies 1001D) were pre-incubated with 2.4µg of either anti H3K4me3 (Diagenode pAb003-050, lot # A5051-001P) or H3K27me3 (Millipore 07-449, lot # 1999681) in ChIP lysis buffer. Lysates were incubated with preformed bead/antibody overnight at 4C with mixing. The chromatin/bead/antibody complexes were washed sequentially with lysis buffer three times, DOC buffer once, and TE buffer once, followed by a transfer to a fresh PCR tube. Chromatin was eluted using elution buffer (1% SDS, 0.1M NaHCO3). IP and Input samples were treated with RNaseA followed by Proteinase K treatment. Cross-linking was reversed by incubating overnight at 65C while shaking. IP-DNA and Inputs were purified using a MinElute PCR Purification Kit (Qiagen 28004).
Libraries were generated using the ThruPLEX-FD Prep Kit (Rubicon Genomics R40048) with 20 cycles of amplification for IP-DNA and 15 cycles for Input DNA.

tag: strain/background

value: transgenic Oct4:GFP B6 crossed to Swiss-Webster

value: primordial germ cells (PGCs)

tag: chip antibody

tag: library amplification cycles


title: PGC_H3K27me3_ChIPSeq

description:
Chromatin IP against H3K27me3 (Millipore 07-449. lot # 1999681)
This Sample represents 2 replicates.

source_name: E11.5 Primordial Germ Cells, H3K27me3 ChIP


title: PGC_Input_ChIPSeq

description:
Input DNA
This Sample represents 2 replicates.

source_name: E11.5 Primordial Germ Cells, input


title: HIV-1Tg_HIP_Saline rep8

city: Charlottesville

first: Shaolin

last: Wang

state: MD

address: 1670 Discovery Dr. Suite

department: Psychiatry

institute: University of Virginia

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rn4 whole genome using tophat and bowtie 1.04 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflink program.
Genome_build: Rn4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Rattus norvegicus

extract_protocol:
PFC, STR and HIP were removed, flash frozen on dry ice, and RNA was extracted using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Either nicotine (0.25 mg/ml) or saline (1 ml/kg of body weight) was administered twice a day (7:00 AM and 4:00 PM) by subcutaneous injection with a 23-gauge/1-cc syringe for 17 days.

value: Hippocampus (HIP)

tag: tissue type

value: Disease model


title: HIV-1Tg_HIP_Saline rep10


title: HIV-1Tg_HIP_Saline rep9


title: HIV-1Tg_HIP_Saline rep6


title: HIV-1Tg_HIP_Saline rep3


title: HIV-1Tg_HIP_Saline rep12


title: HIV-1Tg_HIP_Saline rep2


title: HIV-1Tg_HIP_Saline rep7


title: HIV-1Tg_HIP_Saline rep1


title: HIV-1Tg_HIP_Nicotine rep12


title: HIV-1Tg_HIP_Saline rep11


title: HIV-1Tg_HIP_Saline rep4


title: HIV-1Tg_HIP_Nicotine rep11


title: HIV-1Tg_HIP_Nicotine rep10


title: HIV-1Tg_HIP_Nicotine rep9


title: HIV-1Tg_HIP_Nicotine rep8


title: HIV-1Tg_HIP_Nicotine rep6


title: pSM33-3hr-Xist-R1

value: 3 hours

value: male


title: HIV-1Tg_HIP_Nicotine rep5


title: HIV-1Tg_HIP_Nicotine rep7


title: HIV-1Tg_HIP_Nicotine rep3


title: HIV-1Tg_HIP_Nicotine rep4


title: HIV-1Tg_STR_Saline rep12

value: Striatum (STR)


title: HIV-1Tg_HIP_Nicotine rep2


title: HIV-1Tg_STR_Saline rep10


title: HIV-1Tg_HIP_Nicotine rep1


title: HIV-1Tg_STR_Saline rep9


title: HIV-1Tg_STR_Saline rep8


title: HIV-1Tg_STR_Saline rep7


title: HIV-1Tg_STR_Saline rep5


title: HIV-1Tg_STR_Saline rep3


title: HIV-1Tg_STR_Saline rep2


title: HIV-1Tg_STR_Saline rep4


title: HIV-1Tg_STR_Saline rep1


title: HIV-1Tg_HIP_Saline rep5


title: HIV-1Tg_STR_Nicotine rep12


title: HIV-1Tg_STR_Nicotine rep8


title: HIV-1Tg_STR_Nicotine rep10


title: HIV-1Tg_STR_Nicotine rep7


title: HIV-1Tg_STR_Nicotine rep11


title: HIV-1Tg_STR_Nicotine rep3


title: HIV-1Tg_STR_Nicotine rep6


title: HIV-1Tg_STR_Nicotine rep4


title: HIV-1Tg_STR_Nicotine rep1


title: HIV-1Tg_STR_Nicotine rep5


title: HIV-1Tg_PFC_Saline rep12

value: Prefrontal cortex (PFC)


title: HIV-1Tg_STR_Nicotine rep2


title: HIV-1Tg_PFC_Saline rep11


title: HIV-1Tg_STR_Saline rep11


title: HIV-1Tg_PFC_Saline rep9


title: HIV-1Tg_PFC_Saline rep7


title: HIV-1Tg_STR_Saline rep6


title: HIV-1Tg_PFC_Saline rep5


title: HIV-1Tg_STR_Nicotine rep9


title: HIV-1Tg_PFC_Saline rep1


title: HIV-1Tg_PFC_Nicotine rep12


title: HIV-1Tg_PFC_Saline rep2


title: HIV-1Tg_PFC_Nicotine rep11


title: HIV-1Tg_PFC_Nicotine rep10


title: HIV-1Tg_PFC_Nicotine rep7


title: HIV-1Tg_PFC_Nicotine rep6


title: HIV-1Tg_PFC_Nicotine rep4


title: HIV-1Tg_PFC_Nicotine rep5


title: HIV-1Tg_PFC_Nicotine rep2


title: F344_HIP_Saline rep12

value: Normal


title: HIV-1Tg_PFC_Nicotine rep1


title: F344_HIP_Saline rep10


title: F344_HIP_Saline rep11


title: F344_HIP_Saline rep9


title: HIV-1Tg_PFC_Nicotine rep3


title: F344_HIP_Saline rep8


title: HIV-1Tg_PFC_Saline rep8


title: F344_HIP_Saline rep7


title: HIV-1Tg_PFC_Saline rep6


title: F344_HIP_Saline rep6


title: HIV-1Tg_PFC_Saline rep4


title: F344_HIP_Saline rep5


title: HIV-1Tg_PFC_Saline rep3


title: F344_HIP_Saline rep3


title: F344_HIP_Saline rep2


title: HIV-1Tg_PFC_Nicotine rep9


title: F344_HIP_Saline rep4


title: F344_HIP_Nicotine rep12


title: F344_HIP_Nicotine rep9


title: F344_HIP_Saline rep1


title: HIV-1Tg_PFC_Saline rep10


title: HIV-1Tg_PFC_Nicotine rep8


title: F344_HIP_Nicotine rep7


title: F344_HIP_Nicotine rep10


title: F344_HIP_Nicotine rep2


title: F344_HIP_Nicotine rep3


title: F344_STR_Saline rep12


title: F344_HIP_Nicotine rep6


title: F344_HIP_Nicotine rep4


title: F344_STR_Saline rep10


title: F344_HIP_Nicotine rep5


title: F344_STR_Saline rep11


title: F344_STR_Saline rep5


title: F344_STR_Saline rep6


title: F344_STR_Saline rep8


title: F344_STR_Saline rep9


title: F344_STR_Saline rep7


title: F344_STR_Saline rep4


title: F344_STR_Saline rep3


title: F344_HIP_Nicotine rep11


title: F344_STR_Saline rep2


title: F344_STR_Nicotine rep11


title: F344_STR_Nicotine rep10


title: F344_STR_Saline rep1


title: F344_STR_Nicotine rep12


title: F344_STR_Nicotine rep9


title: F344_HIP_Nicotine rep8


title: F344_STR_Nicotine rep4


title: F344_STR_Nicotine rep6


title: F344_STR_Nicotine rep5


title: F344_HIP_Nicotine rep1


title: F344_STR_Nicotine rep3


title: F344_STR_Nicotine rep2


title: F344_PFC_Saline rep8


title: F344_PFC_Saline rep9


title: F344_PFC_Saline rep10


title: F344_STR_Nicotine rep1


title: F344_PFC_Saline rep7


title: F344_PFC_Saline rep12


title: F344_PFC_Saline rep11


title: F344_PFC_Saline rep2


title: F344_PFC_Saline rep4


title: F344_STR_Nicotine rep8


title: F344_PFC_Saline rep1


title: F344_STR_Nicotine rep7


title: F344_PFC_Saline rep3


title: F344_PFC_Saline rep5


title: F344_PFC_Nicotine rep9


title: F344_PFC_Nicotine rep10


title: F344_PFC_Saline rep6


title: F344_PFC_Nicotine rep11


title: F344_PFC_Nicotine rep7


title: F344_PFC_Nicotine rep6


title: F344_PFC_Nicotine rep4


title: F344_PFC_Nicotine rep8


title: F344_PFC_Nicotine rep5


title: F344_PFC_Nicotine rep2


title: F344_PFC_Nicotine rep1


title: F344_PFC_Nicotine rep3


title: T+S wild-type Bis-seq

city: Taipei

first: Pao-Yang

last: Chen

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
BS-seq reads were aligned to the TAIR10 genome assembly using BS Seeker, allowing up to 10 mismatches.
Alignments with three consecutive methylated non-CG sites are removed.
If multiple alignments mapped to the same location only one is kept.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id (seearabidopsis_tair10.fa.log); column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

organism: Arabidopsis thaliana

source_name: Arabidopsis mature leaves

extract_protocol:
Genomic DNA was isolated with DNeasy Plant Mini Kit (QIAGEN) from mature leaves
Briefly, sonicated DNA was end repaired with NEBnext End Repair module (New England Biolabs), adenylated, and ligated to TruSeq barcoded adaptors (illumina) with T4 DNA ligase. Following purification, samples were bisulfite converted with MethylCode Kit (Invitrogen) and then PCR amplified using Pfu Cx Turbo (Agilent) using the following PCR conditions (2 min at 95°C, 4 cycles of 15sec at 98°C, 30sec at 60°C, 4 min at 72°C and 10min at 72°C).

tag: genotype

value: wild type

value: mature leaves

tag: transgene

value: two-component transgene silencing (T+S)

tag: genetic background


title: Control 30'

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

data_processing:
Basecalls performed using Abi 5500xl ICS (Instrument Controller version 2011.09)
Data were filtered using the following specifications: minimum number of nucleotides in reads = 50
RNA reads were aligned to the NC_003037/NC_003047/NC_003078 genome assembly using CLC Genomics Workbench version 4.7.2 with the following configurations :Additional downstream bases = 0,Exon discovery = Yes,Minimum read count fusion gene table = 5,Minimum length of putative exons = 50,Minimum number of reads = 10,Maximum number of mismatches (short reads) = 2,Organism type = Prokaryote,Use annotations for gene and transcript identification = Yes,Expression level possible values: Genes, Transcripts = Genes,Use strand specific assembly = Yes,Unspecific match limit = 10,Additional upstream bases = 0,Use colorspace encoding = Yes,Minimum exon coverage fraction = 0.2,Minimum length fraction (long reads) = 0.5, Minimum similarity fraction (long reads) = 0.8,  Expression value = Read Per Kilobase of exon Model value
rRNA and tRNA genes were removed from furher analysis
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: NC_003037/NC_003047/NC_003078
Supplementary_files_format_and_content: Excel file include RPKM values for each Sample and all gene identified by LocusTag

organism: Sinorhizobium meliloti 1021

source_name: bacterial culture

growth_protocol: Bacterial cultures in the exponential growth phase were re-diluted and grown to early logarithmic phase (OD600=0.1) in the modified LSM medium in 40 ml volume.

extract_protocol:
Total RNA was purified from samples using the RiboPure Bacteria Kit (Ambion). Residual DNA was removed by using RQ1 RNase-Free DNase (PROMEGA).
RNAs from the three biological replicates were pooled. Before library preparation, ribosomal RNAs were removed using the Ribo-Zero™ rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). Library preparation and RNA sequencing were performed by using the dedicated kits and the SOLiD4 sequencer, respectively, from Life Technologies.

treatment_protocol: Sterile water (untreated control) or NCR247 or NCR335 were added to a final concentration of 10 mg/L.  Three biological replicates from each treatment were incubated with vigorous shaking for 10 and 30 minutes.

tag: treatment

value: Not treated

tag: treatment time point

value: 30 minutes


title: NCR335 10'

value: 10 minutes

tag: strain


title: NCR335 30'


title: R. sphaeroides 2.4.1 microaerob

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences
Size filtering: discarding reads shorter than 12 nt
Read mapping using segemehl version 0.12.0
Genome_build: CP000143.1, CP000144.1, CP000145.1, CP000146.1, CP000147.1, DQ232586.1, DQ232587.1
Supplementary_files_format_and_content: wiggle
Supplementary_files_format_and_content: Unnormalized or normalized read coverages in wiggle format (*_forward.wig = forward strand; *_minus.wig= minus strand)

organism: Cereibacter sphaeroides 2.4.1

source_name: bacterial cells

growth_protocol: R. sphaeroides strains grown anaerobically or microaerobically in presence and absence of iron

extract_protocol:
Total RNA was isolated using the hot phenol method followed by one (Northern) or two (microarray analysis and RNAseq) chloroform-isoamyl alcohol treatments and precipitation with sodium acetate and ethanol. RNA was resolved in RNase free water (Roth) and concentrations were determined at a NanoDrop 1000 Spectrophotometer (Peqlab). The sample was treated with DNaseI (Invitrogen) to remove DNA
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina

treatment_protocol: R. sphaeroides was grown without external iron but with the iron chelator 2,2’-dipyridyl (30 µM). Anaerobic growth was provided using dimethyl sulfoxide (DMSO) as electron acceptor at a final concentration of 60 mM.

tag: growth condition

value: microaerob


title: R. sphaeroides 2.4.1 iron depletion microaerob

value: iron depletion microaerob


title: F344_PFC_Nicotine rep12

tag: tissue


title: R. sphaeroides 2.4.1 anaerob

description:
Note from submitter: R._sphaeroides_2.4.1_anaerob_forward.wig and R._sphaeroides_2.4.1_anaerob_div_by_4349519.0_multi_by_4349519.0_forward.wig are identical.
They are the same files as for the mentioned file the normalization leads to the same outcome as without the normalizatoin- still I would keep it in the set as people usually load all normalized files together into a genome browser and might be confused if those are missing.

value: anaerob


title: R. sphaeroides 2.4.1 iron depletion anaerob

value: iron depletion anaerob


title: NCR247 10'


title: H3K27me1 Millipore OR Head Nuclei D.melanogaster Input Rep1

status: Public on May 28 2013

city: Toronto

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

description: Served as Input for: 2360.enrichment.clusters.gff3

data_processing: Bowtie alignment protocol. Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.Reads that passed default parameters of the Illumina quality filter were mapped with Bowtie 0.12.7. The reference sequence used to built an index for mapping was the Flybase reference r5.22. The reference index was created using the bowtie-build function with default parameters. Reads were mapped using  -n 2 -l 28 -e 70 -k 1 -m 10 --best in Bowtie (-n 2, -l 28, -e 70 default). Parameters-n INT number of allowed mismatch-l INT seed length-e INT maximum permitted total of quality values at all mismatched read positions-m INT suppress all alignments for a particular read or pair if more than INT reportable alignments-k INT report up to INT valid alignments--best report alignments in best-to worst orderReads were converted to SAM formant using the bowtie2sam.pl script provided by the DCC. SPP Peak calling protocol. The aligned reads were called using SPP R package (ver.1.10, Kharchenko et al., Nat.Biotech 2008). The binding characteristics and tag shift were estimated using SPP get.binding.characteristics() function. The reads showing abnormality were removed using SPP remove.local.tag.anomalies() function. The regions of enrichment were identified as continuous blocks of positions that exhibit significant enrichment of IP over input reads. The significance of enrichment was assessed within a 1Kb window around each point using a Poisson model. A position was considered significantly enriched if the number of IP read counts was significantly higher (Z-score > 3) than the number of input read counts, after adjusting for the total number of reads sequenced in IP and input measurements. For each replicate set, if replicates were consistent (>80% agreement for top 40% of peaks/enrichment clusters), reads in each replicates were combined and enrichment regions were called as described above.  Processed data are obtained using following parameters: genome version is FlyBase r5

organism: Drosophila melanogaster

source_name: H3K27me1 Millipore OR Head Nuc Input expt.2352

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Collection of fly heads from whole adults using sieves of varying sizes.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

tag: developmental stage

value: Mixed Adult


title: BAT-DIFF

city: Bonn

first: Franziska

last: Siegel

address: Sigmund-Freud-Str. 25

department: Institute of Pharmacology and Toxicology

institute: University of Bonn

description: MSCs in vitro differentiated to mature adipocytes

data_processing:
Sequenced reads were trimmed for adaptor sequences (5'-ends as well as poly(A) induced 3'-ends) and aggregated if identical
Temporary elimination of A's out of the sequences as well as from the mirBAse-entries used for annotation (huge fluorescent signals of poly-A-tails could sometimes introduce false additional A's in adjacent sequences)
Annotation by sequence comparison between the read sequences and the miRBase-entries (pretreated as described above)
Reviewing the results regarding the 'non-trimmed' reads and miRBase-entries (containing A’s again but no adapter-sequences) and manual elimination of the obviously wrong annotated sequences
Aggregation and counting of identical annotations
total counts were calculated
Genome_build: miRBase 10
Supplementary_files_format_and_content: tab-delimited text files include total counts for each microRNA

source_name: BAT-DIFF

growth_protocol: MSCs were isolated from the stromal vascular fraction (SVF) of brown adipose tissue. This tissue was dissected from newborn C57BL/6 mice.

extract_protocol:
Total RNA was extracted with mirVana miRNA isolation kit (Ambion); subsequent fractionation of miRNAs was done by means of PAA gel electrophoresis
Poly-A-tailing of the miRNAs; ligation of an RNA-adapter to the 5'-end; first-strand cDNA-synthesis using poly(T)-adapter; addition ot the complete flanking sequences while PCR-amplification; final purification of the PCR-product by means of agarose gel electrophoresis

treatment_protocol: For in vitro differentiation to mature brown adipocytes, MSCs were seeded in 6 well plates and grown to confluency. Differentiation was induced by treatment with an adipogenic cocktail containing insulin, IBMX, dexamethasone and T3. Cells were differentiated for a period of 8 days and then harvested for analysis. For a detailed differentiation protocol see following publication: Haas, B., P. Mayer, K. Jennissen, D. Scholz, M. Berriel Diaz, W. Bloch, Herzig, R. Fassler and A. Pfeifer (2009). Protein kinase G controls brown fat cell differentiation and mitochondrial biogenesis. Sci Signal 2(99): ra78

tag: cell type

value: mesenchymal stem cells (MSCs)

value: brown adipose tissue (BAT)

tag: age

value: newborn/ p0


title: H3K27me1 Millipore OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2361.enrichment.clusters.gff3

source_name: H3K27me1 Millipore OR Head Nuc Input expt.2353


title: H3K27me2 Ab24684 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1956.enrichment.clusters.gff3

source_name: H3K27me2 Ab24684 14-16 hr OR Emb Input expt.1961

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: Embryo 14-16hr OR


title: H3K23ac 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K23ac 14-16 hr OR Emb ChIP expt.2483


title: H3K27me2 Ab24684 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1974.enrichment.clusters.gff3

source_name: H3K27me2 Ab24684 14-16 hr OR Emb Input expt.1823


title: Control 10'


title: H3K23ac 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K23ac 14-16 hr OR Emb ChIP expt.2482


title: H3K18Ac new lot 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K18Ac new lot 14-16 hr OR Emb ChIP expt.2489


title: H3K27me1 Millipore OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K27me1 Millipore OR Head Nuc ChIP expt.2360


title: H3 antibody3 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3 antibody3 OR Head Nuc ChIP expt.2189


title: H3 antibody3 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3 antibody3 OR Head Nuc ChIP expt.2190


title: BAT-MSC

description: MSCs isolated from BAT

source_name: BAT-MSC


title: H3K23ac 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2482.enrichment.clusters.gff3

source_name: H3K23ac 14-16 hr OR Emb Input expt.1913


title: NCR247 30'


title: H3K18Ac new lot 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K18Ac new lot 14-16 hr OR Emb ChIP expt.2490


title: H3 antibody3 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2190.enrichment.clusters.gff3

source_name: H3 antibody3 OR Head Nuc Input expt.2188


title: H3K18Ac new lot 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2490.enrichment.clusters.gff3

source_name: H3K18Ac new lot 14-16 hr OR Emb Input expt.2492


title: H3 antibody3 L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3 antibody3 L3 Nuc ChIP expt.2242

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: 3rd Instar Larvae


title: H3 antibody3 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2189.enrichment.clusters.gff3

source_name: H3 antibody3 OR Head Nuc Input expt.2187

value: wild type


title: H3 antibody3 L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3 antibody3 L3 Nuc ChIP expt.2241


title: H3 antibody3 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2242.enrichment.clusters.gff3

source_name: H3 antibody3 L3 Nuc Input expt.2224


title: H3 antibody3 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2241.enrichment.clusters.gff3

source_name: H3 antibody3 L3 Nuc Input expt.2222


title: H3 antibody3 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3 antibody3 14-16 hr OR Emb ChIP expt.2036


title: H3 antibody3 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3 antibody3 14-16 hr OR Emb ChIP expt.2037


title: H3K27me1 Millipore OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K27me1 Millipore OR Head Nuc ChIP expt.2361


title: H3K23ac 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2483.enrichment.clusters.gff3

source_name: H3K23ac 14-16 hr OR Emb Input expt.2025


title: H3K18Ac new lot 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2489.enrichment.clusters.gff3

source_name: H3K18Ac new lot 14-16 hr OR Emb Input expt.2491


title: H3 antibody3 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2037.enrichment.clusters.gff3

source_name: H3 antibody3 14-16 hr OR Emb Input expt.2025


title: H3 antibody3 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2036.enrichment.clusters.gff3

source_name: H3 antibody3 14-16 hr OR Emb Input expt.2024


title: H2B-ubiq NRO3 14-16 hr OR Embryo D.melanogaster ChIP Rep3

source_name: H2B-ubiq NRO3 14-16 hr OR Emb ChIP expt.2505


title: H2B-ubiq NRO3 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H2B-ubiq NRO3 14-16 hr OR Emb ChIP expt.2504


title: H2B-ubiq NRO3 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H2B-ubiq NRO3 OR Head Nuc ChIP expt.2297


title: H2B-ubiq NRO3 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1708.enrichment.clusters.gff3

source_name: H2B-ubiq NRO3 14-16 hr OR Emb Input expt.1729


title: H2B-ubiq NRO3 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2504.enrichment.clusters.gff3

source_name: H2B-ubiq NRO3 14-16 hr OR Emb Input expt.2506


title: H2B-ubiq NRO3 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H2B-ubiq NRO3 OR Head Nuc ChIP expt.2298


title: H2B-ubiq NRO3 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H2B-ubiq NRO3 14-16 hr OR Emb ChIP expt.1708


title: H2B-ubiq NRO3 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2297.enrichment.clusters.gff3

source_name: H2B-ubiq NRO3 OR Head Nuc Input expt.2305


title: H2AV 9751 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H2AV 9751 14-16 hr OR Emb ChIP expt.2472


title: H2AV 9751 14-16 hr OR Embryo D.melanogaster ChIP Rep3

source_name: H2AV 9751 14-16 hr OR Emb ChIP expt.2473


title: H2AV 9751 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2473.enrichment.clusters.gff3

source_name: H2AV 9751 14-16 hr OR Emb Input expt.1658


title: H2B-ubiq NRO3 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2298.enrichment.clusters.gff3

source_name: H2B-ubiq NRO3 OR Head Nuc Input expt.2306


title: H2AV 9751 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H2AV 9751 14-16 hr OR Emb ChIP expt.1706


title: H2B-ubiq NRO3 14-16 hr OR Embryo D.melanogaster Input Rep3

description: Served as Input for: 2505.enrichment.clusters.gff3

source_name: H2B-ubiq NRO3 14-16 hr OR Emb Input expt.2507


title: H1 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H1 OR Head Nuc ChIP expt.2293


title: H2AV 9751 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2472.enrichment.clusters.gff3

source_name: H2AV 9751 14-16 hr OR Emb Input expt.1657


title: H1 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H1 OR Head Nuc ChIP expt.2294


title: H2AV 9751 14-16 hr OR Embryo D.melanogaster Input Rep3

description: Served as Input for: 1706.enrichment.clusters.gff3

source_name: H2AV 9751 14-16 hr OR Emb Input expt.1707


title: H1 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2293.enrichment.clusters.gff3

source_name: H1 OR Head Nuc Input expt.2305


title: dRING Q3200 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1819.enrichment.clusters.gff3

source_name: dRING Q3200 14-16 hr OR Emb Input expt.1815


title: dMi-2 Q4443 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: dMi-2 Q4443 14-16 hr OR Emb ChIP expt.2447


title: dRING Q3200 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2065.enrichment.clusters.gff3

source_name: dRING Q3200 14-16 hr OR Emb Input expt.2062


title: dRING Q3200 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: dRING Q3200 14-16 hr OR Emb ChIP expt.1819


title: H1 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2294.enrichment.clusters.gff3

source_name: H1 OR Head Nuc Input expt.2306


title: dRING Q3200 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: dRING Q3200 14-16 hr OR Emb ChIP expt.2065


title: dMi-2 Q4443 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: dMi-2 Q4443 14-16 hr OR Emb ChIP expt.2448


title: dMi-2 Q4443 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2447.enrichment.clusters.gff3

source_name: dMi-2 Q4443 14-16 hr OR Emb Input expt.2307


title: dMi-2 Q4443 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2448.enrichment.clusters.gff3

source_name: dMi-2 Q4443 14-16 hr OR Emb Input expt.2308


title: CTCF 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: CTCF 14-16 hr OR Emb ChIP expt.1825


title: CTCF 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: CTCF 14-16 hr OR Emb ChIP expt.1967


title: CTCF 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1825.enrichment.clusters.gff3

source_name: CTCF 14-16 hr OR Emb Input expt.1823


title: Chro Chriz WR 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: Chro Chriz WR 14-16 hr OR Emb ChIP expt.1711


title: Chro Chriz WR 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: Chro Chriz WR 14-16 hr OR Emb ChIP expt.1721


title: H3K9me2 antibody2 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2267.enrichment.clusters.gff3

source_name: H3K9me2 antibody2 L3 Nuc Input expt.2223


title: H3K9me2 antibody2 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2268.enrichment.clusters.gff3

source_name: H3K9me2 antibody2 L3 Nuc Input expt.2230


title: H2AV 9751 L3 Nuclei D.melanogaster ChIP Rep2

source_name: H2AV 9751 L3 Nuc ChIP expt.2389


title: H3K9me2 antibody2 L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K9me2 antibody2 L3 Nuc ChIP expt.2268


title: H3K4me2-Active motif L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2335.enrichment.clusters.gff3

source_name: H3K4me2-Active motif L3 Nuc Input expt.2331


title: H3K23ac OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K23ac OR Head Nuc ChIP expt.2206


title: H3K4me2-Active motif L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K4me2-Active motif L3 Nuc ChIP expt.2334


title: H3K23ac OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2206.enrichment.clusters.gff3

source_name: H3K23ac OR Head Nuc Input expt.2188


title: H3K4me2-Active motif L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K4me2-Active motif L3 Nuc ChIP expt.2335


title: H3K9me3 new lot L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K9me3 new lot L3 Nuc ChIP expt.2264


title: H3K9me3 new lot L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K9me3 new lot L3 Nuc ChIP expt.2263


title: H2AV 9751 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2389.enrichment.clusters.gff3

source_name: H2AV 9751 L3 Nuc Input expt.2317


title: H3K9me3 new lot L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2263.enrichment.clusters.gff3

source_name: H3K9me3 new lot L3 Nuc Input expt.2228


title: H3K23ac L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K23ac L3 Nuc ChIP expt.2240


title: H3K23ac L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K23ac L3 Nuc ChIP expt.2239


title: H3K9me3 new lot L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2264.enrichment.clusters.gff3

source_name: H3K9me3 new lot L3 Nuc Input expt.2229


title: Chro Chriz WR 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1711.enrichment.clusters.gff3

source_name: Chro Chriz WR 14-16 hr OR Emb Input expt.1729


title: H3K23ac OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K23ac OR Head Nuc ChIP expt.2205


title: H3K4me2-Active motif L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2334.enrichment.clusters.gff3

source_name: H3K4me2-Active motif L3 Nuc Input expt.2330


title: H3K9me2 antibody2 L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K9me2 antibody2 L3 Nuc ChIP expt.2267


title: H3K23ac L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2240.enrichment.clusters.gff3

source_name: H3K23ac L3 Nuc Input expt.2224


title: CTCF 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1967.enrichment.clusters.gff3

source_name: CTCF 14-16 hr OR Emb Input expt.1962


title: H3K23ac L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2239.enrichment.clusters.gff3

source_name: H3K23ac L3 Nuc Input expt.2222


title: H3K36me3 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K36me3 14-16 hr OR Emb ChIP expt.1719


title: H3K36me3 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K36me3 14-16 hr OR Emb ChIP expt.1709


title: H3K36me3 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1719.enrichment.clusters.gff3

source_name: H3K36me3 14-16 hr OR Emb Input expt.1730


title: H2AV 9751 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2388.enrichment.clusters.gff3

source_name: H2AV 9751 L3 Nuc Input expt.2316


title: H2AV 9751 L3 Nuclei D.melanogaster ChIP Rep1

source_name: H2AV 9751 L3 Nuc ChIP expt.2388


title: Chro Chriz WR 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1721.enrichment.clusters.gff3

source_name: Chro Chriz WR 14-16 hr OR Emb Input expt.1730


title: H3K36me3 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1709.enrichment.clusters.gff3

source_name: H3K36me3 14-16 hr OR Emb Input expt.1729


title: H3K9ac OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2207.enrichment.clusters.gff3

source_name: H3K9ac OR Head Nuc Input expt.2187


title: H3K79me2 Abcam ab3594 lot 1 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1978.enrichment.clusters.gff3

source_name: H3K79me2 Abcam ab3594 lot 1 14-16 hr OR Emb Input expt.1961


title: H3K79me2 Abcam ab3594 lot 1 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1970.enrichment.clusters.gff3

source_name: H3K79me2 Abcam ab3594 lot 1 14-16 hr OR Emb Input expt.1962


title: H3K9ac OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K9ac OR Head Nuc ChIP expt.2208


title: HP4 Q4072 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: HP4 Q4072 14-16 hr OR Emb ChIP expt.1649


title: H4K20me1 3rd lot L3 Nuclei D.melanogaster ChIP Rep1

source_name: H4K20me1 3rd lot L3 Nuc ChIP expt.2390


title: Suvar 3-7 Q3448 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: Suvar 3-7 Q3448 14-16 hr OR Emb ChIP expt.2035


title: HP4 Q4072 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1650.enrichment.clusters.gff3

source_name: HP4 Q4072 14-16 hr OR Emb Input expt.1656


title: HP4 Q4072 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: HP4 Q4072 14-16 hr OR Emb ChIP expt.1650


title: H4K20me1 3rd lot L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2391.enrichment.clusters.gff3

source_name: H4K20me1 3rd lot L3 Nuc Input expt.2317


title: H4K20me1 3rd lot L3 Nuclei D.melanogaster ChIP Rep2

source_name: H4K20me1 3rd lot L3 Nuc ChIP expt.2391


title: HP4 Q4072 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1649.enrichment.clusters.gff3

source_name: HP4 Q4072 14-16 hr OR Emb Input expt.1655


title: H3K79me2 Abcam ab3594 lot 1 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K79me2 Abcam ab3594 lot 1 14-16 hr OR Emb ChIP expt.1978


title: H3K23ac OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2205.enrichment.clusters.gff3

source_name: H3K23ac OR Head Nuc Input expt.2187


title: Suvar 3-7 Q3448 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2035.enrichment.clusters.gff3

source_name: Suvar 3-7 Q3448 14-16 hr OR Emb Input expt.2025


title: H3K18Ac new lot OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2209.enrichment.clusters.gff3

source_name: H3K18Ac new lot OR Head Nuc Input expt.2183


title: H3K18Ac new lot OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2210.enrichment.clusters.gff3

source_name: H3K18Ac new lot OR Head Nuc Input expt.2186


title: H3K36me1 L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K36me1 L3 Nuc ChIP expt.2400


title: H3K36me1 L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K36me1 L3 Nuc ChIP expt.2401


title: Suvar 3-7 Q3448 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2034.enrichment.clusters.gff3

source_name: Suvar 3-7 Q3448 14-16 hr OR Emb Input expt.2024


title: H3K36me1 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2401.enrichment.clusters.gff3

source_name: H3K36me1 L3 Nuc Input expt.2404


title: H3K9ac OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2208.enrichment.clusters.gff3

source_name: H3K9ac OR Head Nuc Input expt.2188


title: H3K18Ac new lot OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K18Ac new lot OR Head Nuc ChIP expt.2210


title: H3K36me1 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2400.enrichment.clusters.gff3

source_name: H3K36me1 L3 Nuc Input expt.2402


title: Suvar 3-7 Q3448 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: Suvar 3-7 Q3448 14-16 hr OR Emb ChIP expt.2034


title: H3K18Ac new lot OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K18Ac new lot OR Head Nuc ChIP expt.2209


title: H3K36me3 abcam L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K36me3 abcam L3 Nuc ChIP expt.2260


title: H3K79me2 Abcam ab3594 lot 1 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K79me2 Abcam ab3594 lot 1 14-16 hr OR Emb ChIP expt.1970


title: H3K36me3 abcam L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K36me3 abcam L3 Nuc ChIP expt.2259


title: H3K36me3 abcam L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2260.enrichment.clusters.gff3

source_name: H3K36me3 abcam L3 Nuc Input expt.2226


title: H3K9me2 Ab2 new lot 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K9me2 Ab2 new lot 14-16 hr OR Emb ChIP expt.2039


title: H3K9me2 Ab2 new lot 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K9me2 Ab2 new lot 14-16 hr OR Emb ChIP expt.2038


title: H3K9me2 Ab2 new lot 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2039.enrichment.clusters.gff3

source_name: H3K9me2 Ab2 new lot 14-16 hr OR Emb Input expt.2025


title: H3K9me2 Ab2 new lot 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2038.enrichment.clusters.gff3

source_name: H3K9me2 Ab2 new lot 14-16 hr OR Emb Input expt.2024


title: H3K9me3 abcam 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K9me3 abcam 14-16 hr OR Emb ChIP expt.2077


title: H4K16ac M 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H4K16acM 14-16 hr OR Emb ChIP expt.1710


title: H3K9me3 abcam 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2076.enrichment.clusters.gff3

source_name: H3K9me3 abcam 14-16 hr OR Emb Input expt.1655


title: H3K9me3 abcam 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2077.enrichment.clusters.gff3

source_name: H3K9me3 abcam 14-16 hr OR Emb Input expt.1656


title: H3K9me3 abcam 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K9me3 abcam 14-16 hr OR Emb ChIP expt.2076


title: H4K16ac M 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1710.enrichment.clusters.gff3

source_name: H4K16acM 14-16 hr OR Emb Input expt.1729


title: H4K20me1 3rd lot OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H4K20me1 3rd lot OR Head Nuc ChIP expt.2274


title: HP1 wa191 L3 Nuclei D.melanogaster ChIP Rep1

source_name: HP1 wa191 L3 Nuc ChIP expt.2265


title: H4K20me1 3rd lot OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2275.enrichment.clusters.gff3

source_name: H4K20me1 3rd lot OR Head Nuc Input expt.2271


title: H4K20me1 3rd lot OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H4K20me1 3rd lot OR Head Nuc ChIP expt.2275


title: HP1 wa191 L3 Nuclei D.melanogaster ChIP Rep2

source_name: HP1 wa191 L3 Nuc ChIP expt.2266


title: H4K20me1 3rd lot OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2274.enrichment.clusters.gff3

source_name: H4K20me1 3rd lot OR Head Nuc Input expt.2270


title: HP1 wa191 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2266.enrichment.clusters.gff3

source_name: HP1 wa191 L3 Nuc Input expt.2229


title: H3K9me3 new lot OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K9me3 new lot OR Head Nuc ChIP expt.2216


title: H3K9me3 new lot OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K9me3 new lot OR Head Nuc ChIP expt.2215


title: H3K9me3 new lot OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2216.enrichment.clusters.gff3

source_name: H3K9me3 new lot OR Head Nuc Input expt.2212


title: H3K36me3 abcam L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2259.enrichment.clusters.gff3

source_name: H3K36me3 abcam L3 Nuc Input expt.2225


title: 14-16 hr OR Embryo D.melanogaster H3K36me1 Rep1

source_name: 14-16 hr OR Emb H3K36me1 expt.1714


title: H4K16ac M 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H4K16acM 14-16 hr OR Emb ChIP expt.1720


title: 14-16 hr OR Embryo D.melanogaster H3K36me1 Rep2

source_name: 14-16 hr OR Emb H3K36me1 expt.1724


title: H3K9me3 new lot OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2215.enrichment.clusters.gff3

source_name: H3K9me3 new lot OR Head Nuc Input expt.2211


title: 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1724.enrichment.clusters.gff3

source_name: 14-16 hr OR Emb Input expt.1730


title: H3K9me1 (new lot) 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K9me1 (new lot) 14-16 hr OR Emb ChIP expt.2021


title: 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1714.enrichment.clusters.gff3

source_name: 14-16 hr OR Emb Input expt.1729


title: H4K16ac M 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1720.enrichment.clusters.gff3

source_name: H4K16acM 14-16 hr OR Emb Input expt.1730


title: H3K9me1 (new lot) 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2021.enrichment.clusters.gff3

source_name: H3K9me1 (new lot) 14-16 hr OR Emb Input expt.1656


title: H3K9me1 (new lot) 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K9me1 (new lot) 14-16 hr OR Emb ChIP expt.2020


title: H3K79Me1 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K79Me1 14-16 hr OR Emb ChIP expt.1955


title: H3K79Me1 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K79Me1 14-16 hr OR Emb ChIP expt.1826


title: H3K9me1 (new lot) 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2020.enrichment.clusters.gff3

source_name: H3K9me1 (new lot) 14-16 hr OR Emb Input expt.1655


title: HP1 wa191 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2265.enrichment.clusters.gff3

source_name: HP1 wa191 L3 Nuc Input expt.2228


title: H3K79Me1 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1955.enrichment.clusters.gff3

source_name: H3K79Me1 14-16 hr OR Emb Input expt.1961


title: H3K79Me1 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1826.enrichment.clusters.gff3

source_name: H3K79Me1 14-16 hr OR Emb Input expt.1823


title: H3K27Ac 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K27Ac 14-16 hr OR Emb ChIP expt.1969


title: H3K27Ac 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K27Ac 14-16 hr OR Emb ChIP expt.1952


title: H3K9ac OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K9ac OR Head Nuc ChIP expt.2207


title: H3K27Ac 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1952.enrichment.clusters.gff3

source_name: H3K27Ac 14-16 hr OR Emb Input expt.1961


title: H3K27Ac 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1969.enrichment.clusters.gff3

source_name: H3K27Ac 14-16 hr OR Emb Input expt.1962


title: H4K20me1 3rd lot L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2390.enrichment.clusters.gff3

source_name: H4K20me1 3rd lot L3 Nuc Input expt.2316


title: GAF 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: GAF 14-16 hr OR Emb ChIP expt.1973


title: Psc 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: Psc 14-16 hr OR Emb ChIP expt.1817


title: GAF 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1973.enrichment.clusters.gff3

source_name: GAF 14-16 hr OR Emb Input expt.1823


title: GAF 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: GAF 14-16 hr OR Emb ChIP expt.1951


title: Psc 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1817.enrichment.clusters.gff3

source_name: Psc 14-16 hr OR Emb Input expt.1815


title: Psc 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1949.enrichment.clusters.gff3

source_name: Psc 14-16 hr OR Emb Input expt.1961


title: CP190-HB 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1971.enrichment.clusters.gff3

source_name: CP190-HB 14-16 hr OR Emb Input expt.1823


title: CP190-HB 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: CP190-HB 14-16 hr OR Emb ChIP expt.1971


title: GAF 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1951.enrichment.clusters.gff3

source_name: GAF 14-16 hr OR Emb Input expt.1961


title: Psc 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: Psc 14-16 hr OR Emb ChIP expt.1949


title: CP190-HB 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1963.enrichment.clusters.gff3

source_name: CP190-HB 14-16 hr OR Emb Input expt.1962


title: CP190-HB 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: CP190-HB 14-16 hr OR Emb ChIP expt.1963


title: SU(HW)-HB 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: SU(HW)-HB 14-16 hr OR Emb ChIP expt.1824


title: SU(HW)-HB 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: SU(HW)-HB 14-16 hr OR Emb ChIP expt.1965


title: SU(HW)-HB 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1824.enrichment.clusters.gff3

source_name: SU(HW)-HB 14-16 hr OR Emb Input expt.1823


title: SU(HW)-HB 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1965.enrichment.clusters.gff3

source_name: SU(HW)-HB 14-16 hr OR Emb Input expt.1962


title: Pc 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1948.enrichment.clusters.gff3

source_name: Pc 14-16 hr OR Emb Input expt.1961


title: Pc 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1816.enrichment.clusters.gff3

source_name: Pc 14-16 hr OR Emb Input expt.1815


title: Pc 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: Pc 14-16 hr OR Emb ChIP expt.1816


title: Pc 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: Pc 14-16 hr OR Emb ChIP expt.1948


title: HP1 wa191 14-16 hr OR Embryo D.melanogaster ChIP Rep4

source_name: HP1 wa191 14-16 hr OR Emb ChIP expt.2027


title: HP1 wa191 14-16 hr OR Embryo D.melanogaster ChIP Rep3

source_name: HP1 wa191 14-16 hr OR Emb ChIP expt.2026


title: HP1 wa191 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: HP1 wa191 14-16 hr OR Emb ChIP expt.1914


title: HP1 wa191 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: HP1 wa191 14-16 hr OR Emb ChIP expt.1916


title: HP1 wa191 14-16 hr OR Embryo D.melanogaster Input Rep4

description: Served as Input for: 2027.enrichment.clusters.gff3

source_name: HP1 wa191 14-16 hr OR Emb Input expt.2025


title: HP1 wa191 14-16 hr OR Embryo D.melanogaster Input Rep3

description: Served as Input for: 2026.enrichment.clusters.gff3

source_name: HP1 wa191 14-16 hr OR Emb Input expt.2024


title: HP1 wa191 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1916.enrichment.clusters.gff3

source_name: HP1 wa191 14-16 hr OR Emb Input expt.1915


title: HP1 wa191 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1914.enrichment.clusters.gff3

source_name: HP1 wa191 14-16 hr OR Emb Input expt.1913


title: H3K27me3 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K27me3 14-16 hr OR Emb ChIP expt.1820


title: H3K27me3 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K27me3 14-16 hr OR Emb ChIP expt.1957


title: H3K27me3 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1957.enrichment.clusters.gff3

source_name: H3K27me3 14-16 hr OR Emb Input expt.1961


title: H3K27me3 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1820.enrichment.clusters.gff3

source_name: H3K27me3 14-16 hr OR Emb Input expt.1815