description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=510,Flow cell=B81CG2ABXX,Lane=1,Barcode=TGACCA,Adult, Mixed Male/Female, Eclosion + 1 day,Digestive System
Adult, Mixed Male/Female, Eclosion + 1 day

data_processing:
510_MixMF_1d_dig_sys_B81CG2ABXX_TGACCA_1_pA_plus.gff; genome build: dm3
510_MixMF_1d_dig_sys_B81CG2ABXX_TGACCA_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mixed males and females, eclosion + 1 day, digestive system

value: Digestive System

value: Mixed Male/Female


status: Public on Nov 23 2011

type: SRA

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

country: USA

institute: University of Connecticut Health Center

description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=512,Flow cell=B81CG2ABXX,Lane=1,Barcode=ACAGTG,Adult, Mixed Male/Female, Eclosion + 1 day,Carcass
Adult, Mixed Male/Female, Eclosion + 1 day

library_source: transcriptomic

data_processing:
512_MixMF_1d_carcass_B81CG2ABXX_ACAGTG_1_pA_plus.gff; genome build: dm3
512_MixMF_1d_carcass_B81CG2ABXX_ACAGTG_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

molecule: total RNA

organism: Drosophila melanogaster

source_name: mixed males and females, eclosion + 1 day, carcass

growth_protocol: Oregon R Animals were grown under standard laboratory conditions.

extract_protocol: Total RNA was isolated from tissues dissected from Oregon R animals in biological duplicates. Strand-specific RNA-seq libraries were prepared using pre-release Directional mRNA-seq Library Kits (Illumina). Briefly, poly(A)+ RNA was isolated by oligo-dT selection, fragmented, and treated with phosphatase and polynucleotide kinase to repair the ends. 3’ and 5’ RNA adapters were then sequentially ligated to the RNA fragments and reverse transcribed using a primer complementary to the 3’ linker. The libraries were then PCR amplified. One nanogram of the strand-specific RNA-Seq libraries were reamplified by PCR using a primer complementary to the 5’ adapter and a second primer complementary to the 3’ adapter with six T residues at the 3’ end. After 10 rounds of amplification, the 3’ primer with the T extension was replaced with a 3’ primer complementary to the adapter with a 5’ extension containing a 6 nt index sequence and a sequence complementary to the flow cell primer. After an additional 15 rounds of amplication, the libraries were quantitated, 10-12 libraries were pooled together and sequenced.

treatment_protocol: None.

tag: strain

value: Oregon R

tag: tissue

value: Carcass

tag: development stage

value: Adult, Eclosion + 1 day

tag: gender

tag: flow cell

tag: lane

tag: barcode

value: ACAGTG


title: Testes, Adult Miwi -/ADH [MR71]

status: Public on Nov 30 2011

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
Adult Library#3
Small RNA Miwi IP
read_length:  36

data_processing: Barcodes where removed, and trimmed reads were mapped to the mouse genome mm9. The software used for processing the data (genomic coordinates etc) from the raw data files are in-house tools from Sachidanandam lab. They are described in a publication: Olson, A.J., Brennecke, J., Aravin, A.A., Hannon, G.J. & Sachidanandam, R. Analysis of large-scale sequencing of small RNAs. Pac Symp Biocomput, 126-36 (2008).

organism: Mus musculus

source_name: Testes, Adult Miwi -/ADH

growth_protocol: mice were mated, grown and kept under standard conditions

extract_protocol:
Testes were dissected from male mice washed in and kept until processing in cold phosphate buffered saline solution.
Miwi-associated small RNAs were isolated from mouse testes and libraries prepared by sequential ligation of 5’- and 3’- RNA adapters. Sequencing was for 36 cycles using the Illumina Genome Analyzer IIx.   For RNAseq of round spermatids total RNA was depleted of abundant RNAs like rRNAs using Ribo-Zero kit (Epicentre). Strand-specific RNAseq library was prepared using the ScriptSeq mRNA-seq Library Preparation Kit (Epicentre; Cat no. SS10906). Sequencing was for 76 cycles by the Illumina Genome Analyzer.   For global 5’-RACE library, total RNA from purified round spermatids was depleted of rRNAs using the Ribo-Zero kit (Epicentre). Then Illumina 5’ RNA adapter was ligated to capture pre-existing 5’ ends. After purification using the Absolutely RNA kit (Stratagene), RNA was reverse-transcribed with a random primer and PCR amplified. PCR products of ~200 bp were gel-eluted for sequencing by the Illumina Genome Analyzer (105 cycles).
Most libraries are run in single lanes. Only one is duplexed and barcoded.

tag: developmental stage

value: Adult

value: Testes

tag: genotype/variation

value: Miwi -/ADH


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=559,Flow cell=B81CG2ABXX,Lane=3,Barcode=CGATGT,Adult, Mixed Male/Female, Eclosion + 20 days,Carcass
Adult, Mixed Male/Female, Eclosion + 20 days

data_processing:
559_MixMF_20d_carcass_B81CG2ABXX_CGATGT_3_pA_plus.gff; genome build: dm3
559_MixMF_20d_carcass_B81CG2ABXX_CGATGT_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mixed males and females, eclosion + 20 days, carcass

value: Adult, Eclosion + 20 days

value: CGATGT


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=501,Flow cell=B81CG2ABXX,Lane=1,Barcode=CGATGT,Adult, Mated Female, Eclosion + 1 day,Head
Adult, Mated Female, Eclosion + 1 day

data_processing:
501_AdMateF_1d_head_B81CG2ABXX_CGATGT_1_pA_plus.gff; genome build: dm3
501_AdMateF_1d_head_B81CG2ABXX_CGATGT_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated female, eclosion + 1 day, heads

value: Head

value: Female

tag: mating status

value: Mated


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=515,Flow cell=62GMCAAXX,Lane=8,Barcode=CTTGTA,Adult, Virgin Female, Eclosion + 4 days,Head
Adult, Virgin Female, Eclosion + 4 days

data_processing:
515_AdVirF_4d_head_62GMCAAXX_CTTGTA_8_pA_plus.gff; genome build: dm3
515_AdVirF_4d_head_62GMCAAXX_CTTGTA_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: virgin female, eclosion + 4 days, heads

value: Adult, Eclosion + 4 days

value: Virgin

value: CTTGTA


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=521,Flow cell=B81CG2ABXX,Lane=1,Barcode=CAGATC,Adult, Mated Female, Eclosion + 4 days,Head
Adult, Mated Female, Eclosion + 4 days

data_processing:
521_AdMateF_4d_head_B81CG2ABXX_CAGATC_1_pA_plus.gff; genome build: dm3
521_AdMateF_4d_head_B81CG2ABXX_CAGATC_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated female, eclosion + 4 days, heads

value: CAGATC


title: Global 5' RACE +/- [MR97]

description:
Adult
Global 5'-RACE
read_length:  105

source_name: Global 5' RACE +/-

value: Miwi +/-


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=590,Flow cell=62GMCAAXX,Lane=8,Barcode=GGCTAC,White Pre-Pupae + 2 days,Fat
White Pre-Pupae + 2 days

data_processing:
590_WPP_2d_fat_62GMCAAXX_GGCTAC_8_pA_plus.gff; genome build: dm3
590_WPP_2d_fat_62GMCAAXX_GGCTAC_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: WPP+2d, fat

value: Oregon R

value: Fat

value: White Pre-Pupae + 2 days

value: GGCTAC


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=550,Flow cell=B81CG2ABXX,Lane=2,Barcode=GATCAG,Adult, Mated Female, Eclosion + 20 days,Head
Adult, Mated Female, Eclosion + 20 days

data_processing:
550_AdMateF_20d_head_B81CG2ABXX_GATCAG_2_pA_plus.gff; genome build: dm3
550_AdMateF_20d_head_B81CG2ABXX_GATCAG_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated female, eclosion + 20 days, heads

value: GATCAG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=578,Flow cell=62GMCAAXX,Lane=8,Barcode=GATCAG,Third Instar Larvae,Central Nervous System
Third Instar Larvae

data_processing:
578_L3_CNS_62GMCAAXX_GATCAG_8_pA_plus.gff; genome build: dm3
578_L3_CNS_62GMCAAXX_GATCAG_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: third instar larvae, CNS

value: Central Nervous System

value: Third Instar Larvae


title: Testes, Adult Miwi +/- [MR66]

description:
Adult
Strand-specific RNASeq
read_length:  76

source_name: Testes, Adult Miwi +/-

value: Adult

value: Testes


title: Global 5' RACE -/ADH [MR99]

description:
Adult
Global 5'-RACE
read_length:  105

source_name: Global 5' RACE -/ADH

value: Miwi -/ADH


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=538,Flow cell=62GMCAAXX,Lane=8,Barcode=TTAGGC,Adult, Mated Male, Eclosion + 4 days,Accessory Gland
Adult, Mated Male, Eclosion + 4 days

data_processing:
538_AdMateM_4d_acc_gland_62GMCAAXX_TTAGGC_8_pA_plus.gff; genome build: dm3
538_AdMateM_4d_acc_gland_62GMCAAXX_TTAGGC_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated male, eclosion + 4 days, accessory glands

value: Accessory Gland

value: Male

value: TTAGGC


title: Testes, Adult Miwi -/ADH [MR25]

description:
Adult Library#1
Small RNA Miwi IP
Duplexed run: Reads with no barcode is MR25. Other library has barcode (CGAC)
read_length:  36


title: Testes, Adult Miwi -/ADH [MR68]


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=584,Flow cell=62GMCAAXX,Lane=8,Barcode=TAGCTT,White Pre-Pupae,Fat
White Pre-Pupae

data_processing:
584_WPP_fat_62GMCAAXX_TAGCTT_8_pA_plus.gff; genome build: dm3
584_WPP_fat_62GMCAAXX_TAGCTT_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: WPP, fat body

value: White Pre-Pupae

value: TAGCTT


title: Arabidopsis (bla2 accession) feeding, biological replicate 2

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
GHZ-8_bla2_2_feeding
polyA RNA

data_processing: Each library was sequenced with single end methods to give read lengths of 45 base pairs. After trimming the barcode sequences (7 bp total; 6-base barcode and a T residue), the usable read lengths for alignment to the genome were 38 bp. For gene expression quantification for each sample, read alignments were performed using the Bowtie/Tophat software package; the following parameters were used: -a 5, -i 5, -I 10000, --solexa-quals, -g 1, --segment-mismatches 3, -p 5 with the genome annotation used as prior information. As we used the -g 1 flag, we excluded repetitive mappings from the analysis. The resulting SAM file for each sample was parsed to generate RPKM values based on the 12/10/2010 annotation of the mite genome.

organism: Tetranychus urticae

source_name: mites grown on A. thaliana Bla2

growth_protocol: To examine the response of mites to growth on different hosts, we reared mites on beans (Phaseolus vulgaris cv. 'California Red Kidney', the long-standing host for the London strain) for four days prior to sample collection. At four days, bean plants were washed with a solution of 0.03% Tween 20 in water to collect mites (6 trays with ~450 bean plants were used). The suspension was filtered through sieves of decreasing diameter, and eggs were collected on 0.1 mm sieves (~500,000 eggs). To have a single layer of eggs, the eggs were plated and air-dried on Petri dishes (between 20,000 and 30,000 eggs per plate). Plates were sealed with parafilm and incubated at 27 C under a constant light cycle for 48 h to allow hatching. Larvae were collected after hatching and gently deposited one by one on plants using a wet brush. Three different species of plants were used as hosts for the mite larvae: 1) bean (Phaseolus vulgaris cv. 'California Red Kidney', the standard host for the London strain): 3 replicates x 2 plants (2 plants per pot), 2 weeks old (2 leaves), were inoculated on both leaves with ~600 larvae per plant (~1,200 larvae per replicate); 2) tomato (Solanum lycopersicum; genotype Heinz 1706): 3 replicates x 2 plants (2 plants per pot), 3 weeks old (2 leaves), were inoculated on both leaves with ~600 larvae per plant (~1,200 larvae per replicate); and 3) Arabidopsis thaliana (ecotype Bla-2): 3 replicates x 6 plants (6 plants per pot), 3 weeks old (4 leaves well developed), were inoculated on the entire plant with ~600 larvae per plant (~1,200 larvae per replicate). All plants used were cultivated under the same conditions used for experiments and for rearing mites (16 hour light/8 hour dark, 27 C). Following inoculation with larvae, all of the plants were placed at 27 C under continuous light for 12 hours. After this time, larvae were gently collected one by one with a wet brush, and were transferred to an Eppendorf tube on dry ice. The tube was changed every 30 minutes to liquid nitrogen, and samples were stored at -80 C until RNA was prepared.

extract_protocol: Libraries construction was contracted out to Fasteris SA. At Fasteris SA, barcoded libraries were prepared such that four samples could be run per lane. The quality of starting RNA was assessed prior to library construction at Fasteris SA with an Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA).

value: London

value: whole body

value: males and females

tag: host

value: A. thaliana Bla-2

tag: replicate

value: biological rep 2; technical reps 1 and 2


title: Tomato feeding, biological replicate 1

description:
GHZ-11_tomato2_feeding
polyA RNA

source_name: mites grown on tomato

value: tomato

value: biological rep 1; technical reps 1 and 2


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=505,Flow cell=B81CG2ABXX,Lane=1,Barcode=TTAGGC,Adult, Mated Male, Eclosion + 1 day,Head
Adult, Mated Male, Eclosion + 1 day

data_processing:
505_AdMateM_1d_head_B81CG2ABXX_TTAGGC_1_pA_plus.gff; genome build: dm3
505_AdMateM_1d_head_B81CG2ABXX_TTAGGC_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated male, eclosion + 1 day, heads

value: Oregon R

value: Head

value: Adult, Eclosion + 1 day

value: Mated


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=572,Flow cell=62GMCAAXX,Lane=8,Barcode=ACTTGA,Third Instar Larvae, Wandering Stage,Digestive System
Third Instar Larvae, Wandering Stage

data_processing:
572_L3_Wand_dig_sys_62GMCAAXX_ACTTGA_8_pA_plus.gff; genome build: dm3
572_L3_Wand_dig_sys_62GMCAAXX_ACTTGA_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: third instar larvae, wandering stage, digestive system

value: Digestive System

value: Third Instar Larvae, Wandering Stage

value: ACTTGA


title: Arabidopsis (bla2 accession) feeding, biological replicate 1

description:
GHZ-7_bla2_1_feeding
polyA RNA


title: Tomato feeding, biological replicate 3

description:
GHZ-23_tomato4_feeding
polyA RNA

value: biological rep 3; technical reps 1 and 2


title: Arabidopsis (bla2 accession) feeding, biological replicate 3

description:
GHZ-9_bla2_3_feeding
polyA RNA


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=567,Flow cell=62GMCAAXX,Lane=8,Barcode=CAGATC,Third Instar Larvae, Wandering Stage,Imaginal Disc
Third Instar Larvae, Wandering Stage

data_processing:
567_L3_Wand_imag_disc_62GMCAAXX_CAGATC_8_pA_plus.gff; genome build: dm3
567_L3_Wand_imag_disc_62GMCAAXX_CAGATC_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: third instar larvae, wandering stage, imaginal discs

value: Imaginal Disc

value: CAGATC


title: turt_smrna_larvae_and_nymph

description: Small RNA

data_processing: The original small RNA fastq file was split by barcode allowing up to one mismatch for the respective samples, and adaptor sequences were removed (trimming was performed by Fasteris SA). Afterwards, reads of lengths from 18-28 nucleotides were mapped to the 12/10/2010 release of the spider mite (Tetranychus urticae) genome using MAQ (up to ten matches were allowed to the genome).

source_name: larvae/nymph

growth_protocol: Animals were mass reared on bean plants (Phaseolus vulgaris cv California Red Kidney) in growth chambers at 27C with a 16:8 hour (light/dark) photoperiod. Plants were washed in 0.1% TRITON X detergent solution in 2-liter beakers to release all spider mite life stages. Adult spider mites, embryos and larvae and nymphs were filtered through a series of fine sieves to isolate the various life stages. RNA isolated from larvae and nymphs were combined in equimolar amounts for the generation of a pooled larvae/nymph small RNA library.

extract_protocol: Libraries construction was contracted out to Fasteris SA. Barcoded smRNA libraries were constructed according to their protocol.

value: London

value: larvae and nymph


title: Bean feeding, biological replicate 3

description:
GHZ-3_bean4_feeding
polyA RNA

source_name: mites grown on bean

value: whole body

value: males and females

value: bean


title: Flavo_PolII_8W

city: Bethesda

first: Kambiz

last: Mousavi

state: MD

address: 50 South Drive, Room 1347

department: National Institute of Arthritis and Musculoskeletal and Skin Diseases

institute: National Institutes of Health

description: Chromatin IP against PolII (Flavopiridol treatment)

library_source: genomic

data_processing: ChIPSeq data were mapped to the mouse genome (mm9 version) using ELAND algorithm integrated within Illumina parallel sequencing analyzer software.  For mRNA-Seq, TOPHAT package was used to map the reads to the genome and spliced junctions, Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).

molecule: genomic DNA

source_name: C2C12 myoblasts

extract_protocol: For ChIPSeq, cells were cross-linked in 1% formaldehyde and processed according to Lee, T. I., Johnstone, S. E. & Young, R. A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729-748 (2006).   bfChIP were performed according to Kim, J., Chu, J., Shen, X., Wang, J. & Orkin, S. H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049-1061 (2008).  Purified DNA was processed according to manufacturer's protocol. For mRNASeq, Illumina protocol was followed.

treatment_protocol: Experimental sample: These were C2C12 cells treated with flavopiridol (1 uM)  for 2hrs in differentiation media.  Flavopiridol is from Sigma Aldrich (Catalog # 3055; lot# 100M4723V).

tag: cell line

value: C2C12 myoblasts

tag: agent

value: flavopiridol

tag: chip antibody

value: PolII 8WG16

tag: chip antibody vendor

value: Covance

tag: chip antibody lot#

tag: chip antibody catalog#


title: CTL_Flavo_PolII_8W

description: Chromatin IP against PolII (Control treatment)

treatment_protocol: Control sample: These were C2C12 cells which were placed in differentiation media (DMEM + 2% horse serum + insulin-transferrin-seleniumG) for 6hrs.

tag: strain

value: control


title: Bean feeding, biological replicate 2

description:
GHZ-2_bean2_feeding
polyA RNA

tag: tissue

value: biological rep 2; technical reps 1 and 2


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=553, Flow cell=62GMCAAXX, Lane=8, Barcode=ATCACG, Adult, Mated Male, Eclosion + 20 days, Head
Adult, Mated Male, Eclosion + 20 days

data_processing:
553_AdMateM_20d_head_62GMCAAXX_ATCACG_8_pA_plus.gff; genome build: dm3
553_AdMateM_20d_head_62GMCAAXX_ATCACG_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated male, eclosion + 20 days, heads

value: Oregon R

value: Head

tag: development stage

value: Adult, Eclosion + 20 days

tag: gender

value: Male

value: Mated

value: ATCACG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=513,Flow cell=62GMCAAXX,Lane=8,Barcode=ACAGTG,Adult, Mixed Male/Female, Eclosion + 1 day,Carcass
Adult, Mixed Male/Female, Eclosion + 1 day

data_processing:
513_MixMF_1d_carcass_62GMCAAXX_ACAGTG_8_pA_plus.gff; genome build: dm3
513_MixMF_1d_carcass_62GMCAAXX_ACAGTG_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mixed males and females, eclosion + 1 day, carcass

value: Carcass

value: Adult, Eclosion + 1 day

value: Mixed Male/Female

tag: flow cell

tag: lane

value: ACAGTG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=560,Flow cell=62GMCAAXX,Lane=8,Barcode=GCCAAT,Adult, Mixed Male/Female, Eclosion + 20 days,Carcass
Adult, Mixed Male/Female, Eclosion + 20 days

data_processing:
560_MixMF_20d_carcass_62GMCAAXX_GCCAAT_8_pA_plus.gff; genome build: dm3
560_MixMF_20d_carcass_62GMCAAXX_GCCAAT_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mixed males and females, eclosion + 20 days, carcass

tag: barcode

value: GCCAAT


title: turt_smrna_embryo

description: Small RNA

source_name: embryo

value: London

tag: developmental stage

value: embryo

value: whole body

value: males and females


title: turt_smrna_adult

description: Small RNA

source_name: adult

value: adult


title: Tomato feeding, biological replicate 2

description:
GHZ-12_tomato3_feeding
polyA RNA

value: tomato

value: biological rep 2; technical reps 1 and 2


title: Bean feeding, biological replicate 1

description:
GHZ-1_bean1_feeding
polyA RNA

value: bean

value: biological rep 1; technical reps 1 and 2


title: larvae_techrep1

description:
polyA RNA
r21_l5_larvae_techrep1

data_processing: Reads were mapped to the spider mite genome using the bowtie/tophat software package. Only unique read mappings were allowed, and genic regions overlapping with other gene models were additionally removed from the gene expression calculations due to the lack of strand specificity. SAM alignment files were parsed using custom python scripts to generate RPKM values based on the 12/10/2010 annotation of the mite genome.

source_name: larvae

growth_protocol: Animals were mass reared on bean plants (Phaseolus vulgaris cv California Red Kidney) in growth chambers at 27C with a 16:8 hour (light/dark) photoperiod. Plants were washed in 0.1% TRITON X detergent solution in 2-liter beakers to release all spider mite life stages. Adult spider mites, nymphs, larvae and eggs were filtered through a series of fine sieves to isolate the various life stages.

extract_protocol: Libraries were generated with methods adapted from the Illumina mRNA sample preparation protocol (cat. no 1004894 Rev.A).

value: larvae

tag: technical replicate


title: larvae_techrep2

description:
polyA RNA
r22_l5_larvae_techrep2

tag: host


title: nymph_techrep1

description:
polyA RNA
r21_l7_nymph_techrep1

source_name: nymph

value: nymph


title: embryo_techrep2

description:
polyA RNA
r22_l3_embryo_techrep2


title: nymph_techrep2

description:
polyA RNA
r22_l7_nymph_techrep2


title: embryo_techrep1

description:
polyA RNA
r21_l3_embryo_techrep1


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=545,Flow cell=62GMCAAXX,Lane=8,Barcode=TGACCA,Adult, Mixed Male/Female, Eclosion + 4 days,Carcass
Adult, Mixed Male/Female, Eclosion + 4 days

data_processing:
545_MixMF_4d_carcass_62GMCAAXX_TGACCA_8_pA_plus.gff; genome build: dm3
545_MixMF_4d_carcass_62GMCAAXX_TGACCA_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mixed males and females, eclosion + 4 days, carcass

value: Oregon R

value: Adult, Eclosion + 4 days

value: TGACCA


title: adult_techrep2

description:
polyA RNA
r22_l1_adult_techrep2


title: adult_techrep1

description:
polyA RNA
r21_l1_adult_techrep1


title: Testes, P20 Miwi +/+ [MR10]

description:
P20-WT
Small RNA Miwi IP
read_length:  36

data_processing: Barcodes where removed, and trimmed reads were mapped to the mouse genome mm9. The software used for processing the data (genomic coordinates etc) from the raw data files are in-house tools from Sachidanandam lab. They are described in a publication: Olson, A.J., Brennecke, J., Aravin, A.A., Hannon, G.J. & Sachidanandam, R. Analysis of large-scale sequencing of small RNAs. Pac Symp Biocomput, 126-36 (2008).

source_name: Testes, P20 Miwi +/+

value: Testes

tag: genotype/variation

value: wildtype, Miwi +/+


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=509,Flow cell=62GMCAAXX,Lane=8,Barcode=CGATGT,Adult, Mixed Male/Female, Eclosion + 1 day,Digestive System
Adult, Mixed Male/Female, Eclosion + 1 day

data_processing:
509_MixMF_1d_dig_sys_62GMCAAXX_CGATGT_8_pA_plus.gff; genome build: dm3
509_MixMF_1d_dig_sys_62GMCAAXX_CGATGT_8_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mixed males and females, eclosion + 1 day, digestive system

value: Digestive System

value: Adult, Eclosion + 1 day

value: Mixed Male/Female

value: CGATGT


title: turt_bla2_feeding_rep_2

description:
polyA RNA
r24_l6_turt__bla2_feeding_rep_2

data_processing: Individual biological replicates (77 bp; one per sequencing lane) were mapped to the spider mite genome using the bowtie/tophat software package. Only unique read mappings were allowed, and genic regions overlapping with other gene models were additionally removed from the gene expression calculations due to the lack of strand specificity. SAM alignment files were parsed using custom python scripts to generate RPKM values based on the 12/10/2010 annotation of the mite genome.

source_name: mixed developmental stages, Kondara

growth_protocol: Animals were mass reared on the bean plants (Phaseolus vulgaris cv California Red Kidney) in growth chambers at 27C with a 16:8 hour (light/dark) photoperiod. Mites were then transferred to either bean (handling control) or one of two Arabidopsis accessions: 1) Bla-2, an accession resistant (as assessed by plant damage) to mite herbivory and 2) Kondara, an accession susceptible to mite feeding. Following 24 hours of feeding on the various hosts, mixed stages of mites were collected and pooled according to their treatment conditions into two biological replicates.

treatment_protocol: Mites were transferred from their laboratory host plant, the bean (Phaseolus vulgaris cv California Red Kidney), to either bean (handling control) or one of two Arabidopsis accessions: 1) Bla-2, an accession resistant (as assessed by plant damage) to mite herbivory and 2) Kondara, an accession susceptible to mite feeding. Mites were then collected 24 hours after host transfer.

value: London

value: mixed

value: A. thaliana Kondara

tag: biological replicate


title: turt_bla2_feeding_rep_1

description:
polyA RNA
r24_l3_turt__bla2_feeding_rep_1


title: turt_kon_feeding_rep_2

description:
polyA RNA
r24_l7_turt__kon_feeding_rep_2

source_name: mixed developmental stages, Bla-2

value: A. thaliana Bla-2


title: turt_kon_feeding_rep_1

description:
polyA RNA
r24_l4_turt__kon_feeding_rep_1


title: MT_Suz12_ChIPSeq

description: Chromatin IP against Suz12

data_processing:
Instrument model: Illumina Genome Analyzer Iix
ChIPSeq data were mapped to the mouse genome (mm9 version) using ELAND algorithm integrated within Illumina parallel sequencing analyzer software.  For mRNA-Seq, TOPHAT package was used to map the reads to the genome and spliced junctions, Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).

growth_protocol: C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin.

treatment_protocol: For differentiation, cells were placed in media containing Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% horse serum, penicillin/streptomycin and insulin-Transferrin-selenium-A.

value: 48-hours differentiated Myotubes

tag: chip antibody (epitope/name)

value: Millipore


title: MB_Suz12_ChIPSeq

description: Chromatin IP against Suz12

value: Proliferating Myoblasts


title: MB_RNASeq

description:
mRNA Sequencing from proliferating Myoblasts
MB_RNASeq.fq.tar.gz

tag: chip antibody details (vendor/catalog #)


title: MT_Ezh1i_RNASeq

description:
mRNA Sequencing from confluent myoblast
MT_Ezh1i_RNASeq.fq.tar.gz

value: Confluent Myoblasts


title: pHANEzh1_Ezh1i_PolII_8WG16_ChIPSeq

description:
Chromatin IP against PolII after Ezh1 RNAi (with Ezh1 overexpression)
pHANEzh1_Ezh1i_PolII_8W.fq.gz

value: 6-hours differentiated Myotubes


title: pHAN_CTL_PolII_8WG16_ChIPSeq

description:
Chromatin IP against PolII
pHAN_CTL_PolII_8W.fq.gz


title: MT_RNASeq

description:
mRNA Sequencing from confluent myoblast
MT_RNASeq.fq.tar.gz


title: Ezh1i_Ezh1_ChIPSeq

description:
Chromatin IP against Ezh1 after Ezh1 RNAi
Ezh1i-MT_Ezh1.fq.gz

value: 24-hours differentiated Myotubes

value: Bethyl/custom designed rabbit polyclonal Antibody


title: CTL_Bio_ChIPSeq

description:
Chromatin IP against bfEzh1
CTL_Bio.fq.tar.gz

value: Streptavidin-coupled dynabeads


title: bfEzh1_Bio_ChIPSeq

description:
Chromatin IP against bfEzh1
bfEzh1_Bio.fq.tar.gz


title: MB_Ezh1_ChIPSeq

description:
Chromatin IP against Ezh1
MB_Ezh1.fq.tar.gz


title: MT_Ezh1_ChIPSeq

description:
Chromatin IP against Ezh1
MT_Ezh1.fq.gz


title: Ezh1i_PolII_Ser5_ChIPSeq

description:
Chromatin IP against PolII phospho-Serine 5 afte Ezh1 RNAi
Ezh1i_PolII_S5P.fq.gz


title: CTL_PolII_Ser5_ChIPSeq

description:
Chromatin IP against PolII phospho-Serine 5
CTL_PolII_S5P.fq.gz


title: Ezh1i_PolII_Ser2_ChIPSeq

description:
Chromatin IP against PolII phospho-Serine 2 after Ezh1 RNAi
Ezh1i_PolII_S2P.fq.tar.gz


title: MB_Ezh2_ChIPSeq

description:
Chromatin IP against Ezh2
MB_Ezh2.fq.gz

value: Active Motif/39639


title: CTL_PolII_Ser2_ChIPSeq

description:
Chromatin IP against PolII phospho-Serine 2
CTL_PolII_S2P.fq.tar.gz


title: Ezh1i_PolII_8WG18_ChIPSeq

description:
Chromatin IP against PolII after Ezh1 RNAi
Ezh1i_PolII_8W.fq.gz


title: CTL_PolII_8WG18_ChIPSeq

description:
Chromatin IP against PolII
CTL_PolII_8W.fq.gz


title: MT_PolII_8WG18_ChIPSeq

description:
Chromatin IP against PolII
MT_PolII_8W.fq.tar.gz


title: Ezh1i_H3K36me3_ChIPSeq

description:
Chromatin IP against H3K36me3 after Ezh1 RNAi
Ezh1i_H3K36me3.fq.gz


title: turt_bean_feeding_rep_2

description:
polyA RNA
r24_l5_turt__bean_feeding_rep_2

source_name: mixed developmental stages, bean

value: bean


title: MB_PolII_8WG18_ChIPSeq

description:
Chromatin IP against PolII
MB_PolII_8W.fq.tar.gz


title: CTL_H3K36me3_ChIPSeq

description:
Chromatin IP against H3K36me3
CTL_H3K36me3.fq.gz


title: pHAN_Ezh1i_PolII_8WG16_ChIPSeq

description:
Chromatin IP against PolII after Ezh1 RNAi
pHAN_Ezh1i_PolII_8W.fq.gz


title: turt_bean_feeding_rep_1

description:
polyA RNA
r24_l2_turt__bean_feeding_rep_1


title: MB_H3K27me3_ChIPSeq

description:
Chromatin IP against H3K27me3
MB_H3K27me3.fq.tar.gz


title: MT_H3K4me3_ChIPSeq

description:
Chromatin IP against H3K4me3
MT_H3K4me3.fq.tar.gz


title: MB_H3K4me3_ChIPSeq

description:
Chromatin IP against H3K4me3
MB_H3K4me3.fq.tar.gz


title: Young_ctl_H3K27me3_ChIPSeq

status: Public on Nov 22 2011

city: Chicago

first: Dali

last: Han

state: IL

address: 5801 South Ellis Avenue

department: Department of Chemisty

institute: University of Chicago

description: Young Empty Vector RNAi treated

data_processing: Alignment: Raw data were mapped to the ce6 genome by Soap2.

organism: Caenorhabditis elegans

source_name: Whole worm, young, control, H3K27me3 ChIP

growth_protocol: C. elegans were cultured on plates with 10x condensed food. Young and Old samples were collected on adult days 3 and 10, respectively.

extract_protocol: ChIP-seq library construction, cluster generation and sequencing analysis using the Illumina 1G Genome Analyzer were performed as described by the manufacturer's protocols.

treatment_protocol: Synchronized eggs grown to young adult stage were distributed to RNAi or non-RNAi plates containing 20 ug/ml FUdR to prevent progeny growth. For RNAi, bacteria clones were selected from Ahringer's RNAi feeding bacteria library (Kamath et al, 2003), and dsRNA expression was induced by 1mM IPTG. The same HT115 bacteria carrying the empty L4440 construct were used as controls in all experiments. The worms were cultured at 20oC and transferred to fresh RNAi plates every 4 days to ensure continued efficacy of RNAi knockdown.

value: whole body

tag: age

value: 3 days

tag: treatment

value: vector control

tag: chip antibody


title: Old_ctl_H3K27me3_ChIPSeq

description: Old Empty Vector RNAi treated

source_name: Whole worm, old, control, H3K27me3 ChIP

tag: strain

value: 10 days


title: Old_utx-1_H3K27me3_ChIPSeq

description: Old Utx-1 RNAi treated

source_name: Whole worm, old, Utx-1 RNAi, H3K27me3 ChIP

tag: tissue

value: Utx-1 RNAi


title: total amplified RNA, 2-to-4 cells Ler/Col embryos, sample # MC_LerCol_11

city: Glarus

first: Marc

middle: William

last: Schmid

address: Hauptstrasse 34

institute: MWSchmid GmbH

description: linear amplified

data_processing: 50 base reads generated by SOLiD v3 were aligned to the TAIR8.0 version of the Arabidopsis Col genome using the SOLiD™ System Analysis Pipeline Tool (Corona Lite 4.0r2.0, Applied Biosystems, USA), allowing up to 4 color-space mismatches with the additional rule “count valid adjacent errors as single errors”. For transcriptome profiles, reads were excluded if they mapped to more than one genomic position, mapped at splice junctions or were partially overlapping. Consequently, full-length reads uniquely mapping inside a transcript were taken.

organism: Arabidopsis thaliana

source_name: embryos (dissected)

growth_protocol: Plants were grown under 16h light.

extract_protocol: 1-RNA extraction: PicoPure RNA Isolation Kit (Arcturus). 2-RNA amplification: WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies, USA) producing single-stranded cDNA. 3- Second strand synthesis: poly-A tails added using Terminal Transferase (New England Biolabs, USA) in presence of dATPs (1 PCR cycle using Ex Taq Polymerase , (TaKaRa, Japan), and oligo(dT)12-18   primers (Invitrogen).  4-Library preparation:  from 500 ng ds cDNA, Covaris S2 system (Covaris, Inc.),  sheared into 80–130 bp   fragments , DNA ends were repaired and ligated to SOLiD P1 and P2 adaptors, followed by enrichment by PCR (7 cycles) and a size selection on gel

tag: Stage

value: 2-to-4 cells embryo stage with suspensor (partial)

tag: maternal strain

value: Landsberg erecta (Ler)

tag: maternal genotype/variation

value: wildtype

tag: paternal strain

value: Columbia_0 (Col0)

tag: paternal genotype/variation


title: total amplified RNA, 2-to-4 cells Ler/Col embryos, sample # MC_kypCol_12

description: linear amplified

tag: stage


title: LS180_TCF4_125

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

description: ChIP-DNA

data_processing: ChIP-seq runs were all 36 or 50bp.  All samples were mapped from fastq files using Bowtie [-m 1 -- best] to hg18 [UCSC human genome build 18]. Replicate lanes were validated separately for reproducibility and then combined for greater read depth. Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and QuEST [http://mendel.stanford.edu/sidowlab/downloads/quest/].  Peaks meeting FDR values of 0.1% from both techniques were analyzed for the publication and included in this archive.

organism: Homo sapiens

source_name: cultured CRC cells

growth_protocol: Cells were grown in normal MEM-alpha with 10% standard FBS serum, 1% Non-essential Amino Acids, 1% Sodium Pyruvate and 1% Penicillin-Streptomycin

extract_protocol: ChIP samples were created from 100 million cells per sample. Libraries were created according to Illumina's ChIP-seq sample preparation kit with no variations. For additional protocol details, including antibody information, please see the supplementary file on the Series record.

treatment_protocol: Cells were treated with 10-7M 1,25(OH)2D3 [125] or with ethanol vehicle [Veh] for 3 hours prior to ChIP assay

tag: antibody

tag: cell line

value: LS180 cells

tag: passages


title: LS180_TCF4_Veh

description: ChIP-DNA

value: vehicle control


title: LS180_CEBPb_Veh

description: ChIP-DNA

value: CEBPb


title: LS180_CDX2_125

description: ChIP-DNA


title: LS180_CEBPb_125

description: ChIP-DNA


title: LS180_Input

description: ChIP-DNA

value: input sample


title: LS180_bCat_125

description: ChIP-DNA

value: bCat


title: LS180_RXR_125

description: ChIP-DNA

value: RXR


title: LS180_VDR_125

description: ChIP-DNA

value: VDR


title: MT_H3K27me3_ChIPSeq

description:
Chromatin IP against H3K27me3
MT_H3K27me3.fq.tar.gz

source_name: C2C12 myoblasts

tag: developmental stage

value: 48-hours differentiated Myotubes


title: Rex-D-S-replicate B

status: Public on Nov 21 2011

city: Irvine

first: Anthony

last: James

state: CA

address: 2315 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: University of California, Irvine

description: see replicate A for alignment (.bam file)

data_processing:
Alignment: Sequence reads were obtained and mapped to the Aedes aegypti genome (Vectorbase AaegL1.2) using Bowtie (Langmead et al., 2009) . All reads mapping with two or fewer mismatches were retained.
Image data were processed using the Illumina Standard Pipeline

molecule: polyA RNA

organism: Aedes aegypti

source_name: Rex-D Puerto Rico, sugar fed

extract_protocol: standard Illumina RNA-seq protocol

treatment_protocol: sugar feeding or blood feeding

value: Rex-D Puerto Rico

tag: feeding

value: sugar fed

value: whole body


title: Rex-D-B-replicate B

source_name: Rex-D Puerto Rico, blood-fed

value: blood-fed


title: CTM-B-replicate B

source_name: Chetumal, blood-fed

value: Chetumal


title: CTM-S-replicate A

description: linked .bam file derived from A/B replicates

source_name: Chetumal, sugar fed


title: Rex-D-B-replicate A


title: Rex-D-S-replicate A


title: CTM-S-replicate B


title: CTM-B-replicate A


title: LS180_CDX2_Veh

description: ChIP-DNA


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: ChIP-Seq input analysis of brain (germinal matrix) tissue from HuFGM02 (A03507) using Illumina HiSeq 2000
library name: A03507
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 64-274 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806947_UCSF-UBC.Brain_Germinal_Matrix.Input.HuFGM02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03507-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Germinal Matrix ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Germinal Matrix, Donor HuFGM02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10422
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,595,168
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0024
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0728
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0948
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM806947_UCSF-UBC.Brain_Germinal_Matrix.Input.HuFGM02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03507-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Germinal Matrix, Donor HuFGM02 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10437
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: BGM Input 02 07
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix ChIP-Seq Input Donor HuFGM02 Library A03507 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,595,168
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0024
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0728
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0948
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Brain

tag: histological type

value: Germinal matrix tissue

tag: is tumor

value: No

value: primary tissue

value: brain (germinal matrix) tissue


description:
design description: ChIP-Seq input analysis of fetal brain tissue from HuFNSC01 (A03491) using Illumina HiSeq 2000
library name: A03491
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 74-345 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806948_UCSF-UBC.Fetal_Brain.Input.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03491-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Brain, Donor HuFNSC01 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10419
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,089,859
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.002
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0215
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0475
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.73

**********************************************************************

ANALYSIS FILE NAME: GSM806948_UCSF-UBC.Fetal_Brain.Input.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03491-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Brain, Donor HuFNSC01 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10434
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FB Input 01 91
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain ChIP-Seq Input Donor HuFNSC01 Library A03491 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,089,859
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.002
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0215
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0475
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.73

**********************************************************************

value: female

value: Brain tissue

value: fetal brain tissue


description:
design description: H3K27me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC01 (A03488) using Illumina HiSeq 2000
library name: A03488
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 78-334 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00241,A299-00242
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806945_UCSF-UBC.Fetal_Brain.H3K27me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03488-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Fetal Brain, Donor HuFNSC01 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10420
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,150,415
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0892
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9219
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3305
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM806945_UCSF-UBC.Fetal_Brain.H3K27me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03488-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC01 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10435
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FB H3K27me3 01 88
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K27me3 Donor HuFNSC01 Library A03488 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,150,415
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0892
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9219
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3305
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************


title: LS180_bCat_Veh

description: ChIP-DNA

value: bCat

value: LS180 cells

tag: treatment

value: vehicle control


title: LS180_RXR_Veh

description: ChIP-DNA

value: RXR


title: LS180_VDR_Veh

description: ChIP-DNA

value: VDR


description:
design description: H3K4me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC01 (A03486) using Illumina HiSeq 2000
library name: A03486
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 79-353 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 2
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806943_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03486-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Fetal Brain, Donor HuFNSC01 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10411
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,180,949
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6215
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.6203
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9998
IROC_PERCENTILE: 85
POISSON_SCORE: 0.6223
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM806943_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03486-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC01 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10426
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FB H3K4me3 01 86
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K4me3 Donor HuFNSC01 Library A03486 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,180,949
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6215
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.6203
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9998
IROC_PERCENTILE: 85
POISSON_SCORE: 0.6223
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************


description:
design description: H3K4me1 ChIP-Seq analysis of fetal brain tissue from HuFNSC01 (A03485) using Illumina HiSeq 2000
library name: A03485
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 73-342 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806942_UCSF-UBC.Fetal_Brain.H3K4me1.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03485-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Fetal Brain, Donor HuFNSC01 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10413
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,582,206
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0423
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.182
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.8473
IROC_PERCENTILE: 9
POISSON_SCORE: 0.3392
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.9

**********************************************************************

ANALYSIS FILE NAME: GSM806942_UCSF-UBC.Fetal_Brain.H3K4me1.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03485-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC01 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10428
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FB H3K4me1 01 85
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K4me1 Donor HuFNSC01 Library A03485 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,582,206
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0423
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.182
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.8473
IROC_PERCENTILE: 9
POISSON_SCORE: 0.3392
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.9

**********************************************************************


description:
design description: H3K36me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC02 (A03497) using Illumina HiSeq 2000
library name: A03497
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 15 ug
SIZE_FRACTION: 109-368 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806938_UCSF-UBC.Fetal_Brain.H3K36me3.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03497-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Fetal Brain, Donor HuFNSC02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10425
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,656,457
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0335
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1328
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.8845
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3371
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM806938_UCSF-UBC.Fetal_Brain.H3K36me3.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03497-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC02 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10440
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FB H3K36me3 02 97
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K36me3 Donor HuFNSC02 Library A03497 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,656,457
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0335
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1328
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.8845
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3371
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************


description:
design description: H3K9me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC02 (A03495) using Illumina HiSeq 2000
library name: A03495
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 15 ug
SIZE_FRACTION: 107-396 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806936_UCSF-UBC.Fetal_Brain.H3K9me3.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03495-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Fetal Brain, Donor HuFNSC02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10415
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,962,578
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0664
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1069
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.8381
IROC_PERCENTILE: 45
POISSON_SCORE: 0.269
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM806936_UCSF-UBC.Fetal_Brain.H3K9me3.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03495-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC02 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10430
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FB H3K9me3 02 95
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K9me3 Donor HuFNSC02 Library A03495 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,962,578
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0664
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1069
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.8381
IROC_PERCENTILE: 45
POISSON_SCORE: 0.269
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************


description:
design description: H3K9me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC01 (A03487) using Illumina HiSeq 2000
library name: A03487
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 68-358 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806944_UCSF-UBC.Fetal_Brain.H3K9me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03487-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Fetal Brain, Donor HuFNSC01 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10414
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,057,770
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1623
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.1877
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9115
IROC_PERCENTILE: 86
POISSON_SCORE: 0.4073
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM806944_UCSF-UBC.Fetal_Brain.H3K9me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03487-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC01 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10429
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FB H3K9me3 01 87
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K9me3 Donor HuFNSC01 Library A03487 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,057,770
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1623
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.1877
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9115
IROC_PERCENTILE: 86
POISSON_SCORE: 0.4073
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************


description:
design description: H3K9me3 ChIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A03503) using Illumina HiSeq 2000
library name: A03503
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 15 ug
SIZE_FRACTION: 74-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806941_UCSF-UBC.Brain_Germinal_Matrix.H3K9me3.HuFGM02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03503-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Germinal Matrix Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Germinal Matrix, Donor HuFGM02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10421
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,362,248
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2463
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.2683
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9311
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4288
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.86

**********************************************************************

ANALYSIS FILE NAME: GSM806941_UCSF-UBC.Brain_Germinal_Matrix.H3K9me3.HuFGM02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03503-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10436
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: BGM H3K9me3 02 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix Histone H3K9me3 Donor HuFGM02 Library A03503 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,362,248
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2463
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.2683
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9311
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4288
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.86

**********************************************************************


description:
design description: H3K4me1 ChIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A03501) using Illumina HiSeq 2000
library name: A03501
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 15 ug
SIZE_FRACTION: 94-304 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806939_UCSF-UBC.Brain_Germinal_Matrix.H3K4me1.HuFGM02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03501-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Germinal Matrix Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Germinal Matrix, Donor HuFGM02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10416
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,455,611
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0942
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2172
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9133
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3705
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM806939_UCSF-UBC.Brain_Germinal_Matrix.H3K4me1.HuFGM02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03501-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10431
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: BGM H3K4me1 02 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix Histone H3K4me1 Donor HuFGM02 Library A03501 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,455,611
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0942
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2172
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9133
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3705
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************


description:
design description: H3K27me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC02 (A03496) using Illumina HiSeq 2000
library name: A03496
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 15 ug
SIZE_FRACTION: 99-421 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00241
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM806937_UCSF-UBC.Fetal_Brain.H3K27me3.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03496-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Fetal Brain, Donor HuFNSC02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10423
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,364,210
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0563
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0886
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9636
IROC_PERCENTILE: 78
POISSON_SCORE: 0.2291
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.96

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ANALYSIS FILE NAME: GSM806937_UCSF-UBC.Fetal_Brain.H3K27me3.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03496-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC02 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10438
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FB H3K27me3 02 96
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K27me3 Donor HuFNSC02 Library A03496 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,364,210
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0563
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0886
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9636
IROC_PERCENTILE: 78
POISSON_SCORE: 0.2291
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************